Alex W Hernsdorf, Yuki Amano, Kazuya Miyakawa et al.

The ISME Journal • 2017

Geological sequestration in deep underground repositories is the prevailing proposed route for radioactive waste disposal. After the disposal of radioactive waste in the subsurface, H 2 may be produced by corrosion of steel and, ultimately, radionuclides will be exposed to the surrounding environment. To evaluate the potential for microbial activities to impact disposal systems, we explored the microbial community structure and metabolic functions of a sediment-hosted ecosystem at the Horonobe Underground Research Laboratory, Hokkaido, Japan. Overall, we found that the ecosystem hosted organisms from diverse lineages, including many from the phyla that lack isolated representatives. The majority of organisms can metabolize H 2 , often via oxidative [NiFe] hydrogenases or electron-bifurcating [FeFe] hydrogenases that enable ferredoxin-based pathways, including the ion motive Rnf complex. Many organisms implicated in H 2 metabolism are also predicted to catalyze carbon, nitrogen, iron and sulfur transformations. Notably, iron-based metabolism is predicted in a novel lineage of Actinobacteria and in a putative methane-oxidizing ANME-2d archaeon. We infer an ecological model that links microorganisms to sediment-derived resources and predict potential impacts of microbial activity on H 2 consumption and retardation of radionuclide migration.

Adrien Vigneron, Eric Alsop, B. P. Lomans et al.

The ISME Journal • 2017

Subsurface petroleum reservoirs are an important component of the deep biosphere where indigenous microorganisms live under extreme conditions and in isolation from the Earth's surface for millions of years. However, unlike the bulk of the deep biosphere, the petroleum reservoir deep biosphere is subject to extreme anthropogenic perturbation, with the introduction of new electron acceptors, donors and exogenous microbes during oil exploration and production. Despite the fundamental and practical significance of this perturbation, there has never been a systematic evaluation of the ecological changes that occur over the production lifetime of an active offshore petroleum production system. Analysis of the entire Halfdan oil field in the North Sea (32 producing wells in production for 1-15 years) using quantitative PCR, multigenic sequencing, comparative metagenomic and genomic bins reconstruction revealed systematic shifts in microbial community composition and metabolic potential, as well as changing ecological strategies in response to anthropogenic perturbation of the oil field ecosystem, related to length of time in production. The microbial communities were initially dominated by slow growing anaerobes such as members of the Thermotogales and Clostridiales adapted to living on hydrocarbons and complex refractory organic matter. However, as seawater and nitrate injection (used for secondary oil production) delivered oxidants, the microbial community composition progressively changed to fast growing opportunists such as members of the Deferribacteres, Delta-, Epsilon- and Gammaproteobacteria, with energetically more favorable metabolism (for example, nitrate reduction, H 2 S, sulfide and sulfur oxidation). This perturbation has profound consequences for understanding the microbial ecology of the system and is of considerable practical importance as it promotes detrimental processes such as reservoir souring and metal corrosion. These findings provide a new conceptual framework for understanding the petroleum reservoir biosphere and have consequences for developing strategies to manage microbiological problems in the oil industry.

Yunho Lee, Yunhee Lee, Che Ok Jeon

Scientific Reports • 2019

To isolate bacteria responsible for the biodegradation of naphthalene, BTEX (benzene, toluene, ethylbenzene, and o-, m-, and p-xylene), and aliphatic hydrocarbons in petroleum-contaminated soil, three enrichment cultures were established using soil extract as the medium supplemented with naphthalene, BTEX, or n-hexadecane. Community analyses showed that Paraburkholderia species were predominant in naphthalene and BTEX, but relatively minor in n-hexadecane. Paraburkholderia aromaticivorans BN5 was able to degrade naphthalene and all BTEX compounds, but not n-hexadecane. The genome of strain BN5 harbors genes encoding 29 monooxygenases including two alkane 1-monooxygenases and 54 dioxygenases, indicating that strain BN5 has versatile metabolic capabilities, for diverse organic compounds: the ability of strain BN5 to degrade short chain aliphatic hydrocarbons was verified experimentally. The biodegradation pathways of naphthalene and BTEX compounds were bioinformatically predicted and verified experimentally through the analysis of their metabolic intermediates. Some genomic features including the encoding of the biodegradation genes on a plasmid and the low sequence homologies of biodegradation-related genes suggest that biodegradation potentials of strain BN5 may have been acquired via horizontal gene transfers and/or gene duplication, resulting in enhanced ecological fitness by enabling strain BN5 to degrade all compounds including naphthalene, BTEX, and short aliphatic hydrocarbons in contaminated soil.

Laura Rix, Jasper M. de Goeij, Christina E. Mueller et al.

Scientific Reports • 2016

Shallow warm-water and deep-sea cold-water corals engineer the coral reef framework and fertilize reef communities by releasing coral mucus, a source of reef dissolved organic matter (DOM). By transforming DOM into particulate detritus, sponges play a key role in transferring the energy and nutrients in DOM to higher trophic levels on Caribbean reefs via the so-called sponge loop. Coral mucus may be a major DOM source for the sponge loop, but mucus uptake by sponges has not been demonstrated. Here we used laboratory stable isotope tracer experiments to show the transfer of coral mucus into the bulk tissue and phospholipid fatty acids of the warm-water sponge Mycale fistulifera and cold-water sponge Hymedesmia coriacea, demonstrating a direct trophic link between corals and reef sponges. Furthermore, 21-40% of the mucus carbon and 32-39% of the nitrogen assimilated by the sponges was subsequently released as detritus, confirming a sponge loop on Red Sea warm-water and north Atlantic cold-water coral reefs. The presence of a sponge loop in two vastly different reef environments suggests it is a ubiquitous feature of reef ecosystems contributing to the high biogeochemical cycling that may enable coral reefs to thrive in nutrient-limited (warm-water) and energy-limited (cold-water) environments.

Son A. Hoang, Dane Lamb, Balaji Seshadri et al.

Journal of Hazardous Materials • 2020

Kaustuvmani Patowary, Rupshikha Patowary, Mohan Chandra Kalita et al.

Frontiers in Microbiology • 2016

The intrinsic biodegradability of hydrocarbons and the distribution of proficient degrading microorganisms in the environment are very crucial for the implementation of bioremediation practices. Among others, one of the most favorable methods that can enhance the effectiveness of bioremediation of hydrocarbon-contaminated environment is the application of biosurfactant producing microbes. In the present study, the biodegradation capacities of native bacterial consortia toward total petroleum hydrocarbons (TPH) with special emphasis to poly aromatic hydrocarbons were determined. The purpose of the study was to isolate TPH degrading bacterial strains from various petroleum contaminated soil of Assam, India and develop a robust bacterial consortium for bioremediation of crude oil of this native land. From a total of 23 bacterial isolates obtained from three different hydrocarbons contaminated samples five isolates, namely KS2, PG1, PG5, R1, and R2 were selected as efficient crude oil degraders with respect to their growth on crude oil enriched samples. Isolates KS2, PG1, and R2 are biosurfactant producers and PG5, R1 are non-producers. Fourteen different consortia were designed involving both biosurfactant producing and non-producing isolates. Consortium 10, which comprises two Bacillus strains namely, Bacillus pumilus KS2 and B. cereus R2 (identified by 16s rRNA sequencing) has shown the best result in the desired degradation of crude oil. The consortium showed degradation up to 84.15% of TPH after 5 weeks of incubation, as revealed from gravimetric analysis. FTIR (Fourier transform infrared) and GCMS (Gas chromatography-mass spectrometer) analyses were correlated with gravimetric data which reveals that the consortium has removed a wide range of petroleum hydrocarbons in comparison with abiotic control including different aliphatic and aromatic hydrocarbons.

Dimitri V. Meier, Petra Pjevac, Wolfgang Bach et al.

The ISME Journal • 2017

At deep-sea hydrothermal vents, primary production is carried out by chemolithoautotrophic microorganisms, with the oxidation of reduced sulfur compounds being a major driver for microbial carbon fixation. Dense and highly diverse assemblies of sulfur-oxidizing bacteria (SOB) are observed, yet the principles of niche differentiation between the different SOB across geochemical gradients remain poorly understood. In this study niche differentiation of the key SOB was addressed by extensive sampling of active sulfidic vents at six different hydrothermal venting sites in the Manus Basin, off Papua New Guinea. We subjected 33 diffuse fluid and water column samples and 23 samples from surfaces of chimneys, rocks and fauna to a combined analysis of 16S rRNA gene sequences, metagenomes and real-time in situ measured geochemical parameters. We found Sulfurovum Epsilonproteobacteria mainly attached to surfaces exposed to diffuse venting, while the SUP05-clade dominated the bacterioplankton in highly diluted mixtures of vent fluids and seawater. We propose that the high diversity within Sulfurimonas- and Sulfurovum-related Epsilonproteobacteria observed in this study derives from the high variation of environmental parameters such as oxygen and sulfide concentrations across small spatial and temporal scales.

Gerardo Coppola, Maria Teresa Gaudio, Catia Giovanna Lopresto et al.

Earth Systems and Environment • 2021

Abstract Environmental pollutions are increasing day by day due to more plastic application. The plastic material is going in our food chain as well as the environment employing microplastic and other plastic-based contaminants. From this point, bio-based plastic research is taking attention for a sustainable and greener environment with a lower footprint on the environment. This evaluation should be made considering the whole life cycle assessment of the proposed technologies to make a whole range of biomaterials. Bio-based and biodegradable bioplastics can have similar features as conventional plastics while providing extra returns because of their low carbon footprint as long as additional features in waste management, like composting. Interest in competitive biodegradable materials is growing to limit environmental pollution and waste management problems. Bioplastics are defined as plastics deriving from biological sources and formed from renewable feedstocks or by a variation of microbes, owing to the ability to reduce the environmental effect. The research and development in this field of bio-renewable resources can seriously lead to the adoption of a low-carbon economy in medical, packaging, structural and automotive engineering, just to mention a few. This review aims to give a clear insight into the research, application opportunities, sourcing and sustainability, and environmental footprint of bioplastics production and various applications. Bioplastics are manufactured from polysaccharides, mainly starch-based, proteins, and other alternative carbon sources, such as algae or even wastewater treatment byproducts. The most known bioplastic today is thermoplastic starch, mainly as a result of enzymatic bioreactions. In this work, the main applications of bioplastics are accounted. One of them being food applications, where bioplastics seem to meet the food industry concerns about many the packaging-related issues and appear to play an important part for the whole food industry sustainability, helping to maintain high-quality standards throughout the whole production and transport steps, translating into cleaner and smarter delivery chains and waste management. High perspectives resides in agricultural and medical applications, while the number of fields of applications grows constantly, for example, structural engineering and electrical applications. As an example, bio-composites, even from vegetable oil sources, have been developed as fibers with biodegradable features and are constantly under research.

Kasper Urup Kjeldsen, Lars Schreiber, Casper Thorup et al.

Proceedings of the National Academy of Sciences • 2019

Cable bacteria of the family Desulfobulbaceae form centimeter-long filaments comprising thousands of cells. They occur worldwide in the surface of aquatic sediments, where they connect sulfide oxidation with oxygen or nitrate reduction via long-distance electron transport. In the absence of pure cultures, we used single-filament genomics and metagenomics to retrieve draft genomes of 3 marine Candidatus Electrothrix and 1 freshwater Ca. Electronema species. These genomes contain >50% unknown genes but still share their core genomic makeup with sulfate-reducing and sulfur-disproportionating Desulfobulbaceae, with few core genes lost and 212 unique genes (from 197 gene families) conserved among cable bacteria. Last common ancestor analysis indicates gene divergence and lateral gene transfer as equally important origins of these unique genes. With support from metaproteomics of a Ca. Electronema enrichment, the genomes suggest that cable bacteria oxidize sulfide by reversing the canonical sulfate reduction pathway and fix CO 2 using the Wood-Ljungdahl pathway. Cable bacteria show limited organotrophic potential, may assimilate smaller organic acids and alcohols, fix N 2 , and synthesize polyphosphates and polyglucose as storage compounds; several of these traits were confirmed by cell-level experimental analyses. We propose a model for electron flow from sulfide to oxygen that involves periplasmic cytochromes, yet-unidentified conductive periplasmic fibers, and periplasmic oxygen reduction. This model proposes that an active cable bacterium gains energy in the anodic, sulfide-oxidizing cells, whereas cells in the oxic zone flare off electrons through intense cathodic oxygen respiration without energy conservation; this peculiar form of multicellularity seems unparalleled in the microbial world.

Stefan Dyksma, Lukas Jansen, Claudia Gallert

Microbiome • 2020

Results presented here provide new insights into a remarkable anaerobic digestion ecosystem where acetate catabolism is mainly realized by Bacteria. Metagenomics and enrichment cultivation revealed a core community of diverse and novel uncultured acetate-oxidizing bacteria and point to a particular niche for them in dry fermentation of biowaste. Their genomic repertoire suggests metabolic plasticity besides the potential for syntrophic acetate oxidation. Video Abstract.

Rachel Mackelprang, Alexander Burkert, Monica Haw et al.

The ISME Journal • 2017

In permafrost (perennially frozen ground) microbes survive oligotrophic conditions, sub-zero temperatures, low water availability and high salinity over millennia. Viable life exists in permafrost tens of thousands of years old but we know little about the metabolic and physiological adaptations to the challenges presented by life in frozen ground over geologic time. In this study we asked whether increasing age and the associated stressors drive adaptive changes in community composition and function. We conducted deep metagenomic and 16 S rRNA gene sequencing across a Pleistocene permafrost chronosequence from 19 000 to 33 000 years before present (kyr). We found that age markedly affected community composition and reduced diversity. Reconstruction of paleovegetation from metagenomic sequence suggests vegetation differences in the paleo record are not responsible for shifts in community composition and function. Rather, we observed shifts consistent with long-term survival strategies in extreme cryogenic environments. These include increased reliance on scavenging detrital biomass, horizontal gene transfer, chemotaxis, dormancy, environmental sensing and stress response. Our results identify traits that may enable survival in ancient cryoenvironments with no influx of energy or new materials.

Kelton W. McMahon, Matthew D. McCarthy

Ecosphere • 2016

Abstract Compound‐specific stable isotope analysis ( CSIA ) of individual amino acids ( AA s) has become a powerful analytical tool in trophic ecology. Heavily fractionating “trophic” AA s (e.g., glutamic acid: Glu) provide a robust indicator of trophic transfer, while minimally fractionating “source” AA s (e.g., phenylalanine: Phe) closely reflect the δ 15 N value at the base of the food web (δ 15 N baseline ). Together, the CSIA ‐ AA approach provides an unprecedented ability to disentangle the influences of δ 15 N baseline values and trophic fractionation on consumer nitrogen isotope values. Perhaps the most important assumption underlying CSIA ‐ AA applications to trophic ecology is that trophic fractionation of Glu and Phe, and thus the trophic discrimination factor TDF Glu‐ Phe (Δ 15 N G lu − Δ 15 N P he ), is effectively constant across diverse consumer–resource relationships. To test this assumption, we conducted a comprehensive meta‐analysis of controlled feeding experiments that examined individual AA trophic fractionation (Δ 15 N C‐D ) and resulting TDF Glu‐ Phe values. We found tremendous variability in TDF Glu‐ Phe values from 0‰ to >10‰ across 70 species (317 individuals) and 88 distinct consumer–diet combinations. However, this variability appears to follow predictable patterns driven by two dominant variables: diet quality and mode of nitrogen excretion. Consumers feeding on high‐quality diets (small diet–consumer AA imbalances) tend to have significantly lower TDF Glu‐ Phe values than consumers feeding on low‐quality diets. Similarly, urea/uric acid‐producing consumers also exhibit significantly lower TDF Glu‐ Phe values than their ammonia‐producing counterparts. While these patterns are certainly not universal, together these factors likely explain many of the observed patterns of TDF Glu‐ Phe variability. We provide an overview of the biochemical and physiological mechanisms underpinning AA Δ 15 N C‐D to explain these patterns. There are several seemingly unique systems, including the remarkably consistent TDF Glu‐ Phe values across insect food webs and the isotopically “invisible” trophic transfers in microbial food webs, that may provide additional insight into the influence of diet quality and nitrogen cycling on AA fractionation. In this review, we argue that to realize the full potential of CSIA ‐ AA approaches in trophic ecology, we must embrace the variability in TDF Glu‐ Phe values. This likely requires developing new models of trophic transfer dynamics for some applications, including multi‐ TDF Glu‐ Phe equations that directly incorporate variability in TDF Glu‐ Phe value.

Shichang Kang, Qianggong Zhang, Yun Qian et al.

National Science Review • 2019

The Tibetan Plateau and its surroundings are known as the Third Pole (TP). This region is noted for its high rates of glacier melt and the associated hydrological shifts that affect water supplies in Asia. Atmospheric pollutants contribute to climatic and cryospheric changes through their effects on solar radiation and the albedos of snow and ice surfaces; moreover, the behavior and fates within the cryosphere and environmental impacts of environmental pollutants are topics of increasing concern. In this review, we introduce a coordinated monitoring and research framework and network to link atmospheric pollution and cryospheric changes (APCC) within the TP region. We then provide an up-to-date summary of progress and achievements related to the APCC research framework, including aspects of atmospheric pollution's composition and concentration, spatial and temporal variations, trans-boundary transport pathways and mechanisms, and effects on the warming of atmosphere and changing in Indian monsoon, as well as melting of glacier and snow cover. We highlight that exogenous air pollutants can enter into the TP's environments and cause great impacts on regional climatic and environmental changes. At last, we propose future research priorities and map out an extended program at the global scale. The ongoing monitoring activities and research facilitate comprehensive studies of atmosphere-cryosphere interactions, represent one of China's key research expeditions to the TP and the polar regions and contribute to the global perspective of earth system science.

Stefan Becker, Jan Tebben, Sarah Coffinet et al.

Proceedings of the National Academy of Sciences • 2020

Marine microalgae sequester as much CO 2 into carbohydrates as terrestrial plants. Polymeric carbohydrates (i.e., glycans) provide carbon for heterotrophic organisms and constitute a carbon sink in the global oceans. The quantitative contributions of different algal glycans to cycling and sequestration of carbon remain unknown, partly because of the analytical challenge to quantify glycans in complex biological matrices. Here, we quantified a glycan structural type using a recently developed biocatalytic strategy, which involves laminarinase enzymes that specifically cleave the algal glycan laminarin into readily analyzable fragments. We measured laminarin along transects in the Arctic, Atlantic, and Pacific oceans and during three time series in the North Sea. These data revealed a median of 26 ± 17% laminarin within the particulate organic carbon pool. The observed correlation between chlorophyll and laminarin suggests an annual production of algal laminarin of 12 ± 8 gigatons: that is, approximately three times the annual atmospheric carbon dioxide increase by fossil fuel burning. Moreover, our data revealed that laminarin accounted for up to 50% of organic carbon in sinking diatom-containing particles, thus substantially contributing to carbon export from surface waters. Spatially and temporally variable laminarin concentrations in the sunlit ocean are driven by light availability. Collectively, these observations highlight the prominent ecological role and biogeochemical function of laminarin in oceanic carbon export and energy flow to higher trophic levels.

Kendra L. Daly, Uta Passow, Jeffrey P. Chanton et al.

Anthropocene • 2016

The Deepwater Horizon oil spill was the largest in US history, unprecedented for the depth and volume of oil released, the amount of dispersants applied, and the unexpected, protracted sedimentation of oil-associated marine snow (MOS) to the seafloor. Marine snow formation, incorporation of oil, and subsequent gravitational settling to the seafloor (i.e., MOSSFA: Marine Oil Snow Sedimentation and Flocculent Accumulation) was a significant pathway for the distribution and fate of oil, accounting for as much as 14% of the total oil released. Long residence times of oil on the seafloor will result in prolonged exposure by benthic organisms and economically important fish. Bioaccumulation of hydrocarbons into the food web also has been documented. Major surface processes governing the MOSSFA event included an elevated and extended Mississippi River discharge, which enhanced phytoplankton production and suspended particle concentrations, zooplankton grazing, and enhanced microbial mucus formation. Previous reports indicated that MOS sedimentation also occurred during the Tsesis and Ixtoc-I oil spills; thus, MOSSFA events may occur during future oil spills, particularly since 85% of global deep-water oil exploration sites are adjacent to deltaic systems. We provide a conceptual framework of MOSSFA processes and identify data gaps to help guide current research and to improve our ability to predict MOSSFA events under different environmental conditions. Baseline time-series data and model development are urgently needed for all levels of ecosystems in regions of hydrocarbon extraction to prepare for and respond to future oil spills and to understand the impacts of oil spills on the environment.

Li Li, Kate Maher, Alexis Navarre‐Sitchler et al.

Earth-Science Reviews • 2016

Momme Butenschön, James R. Clark, John Aldridge et al.

Geoscientific model development • 2016

Abstract. The European Regional Seas Ecosystem Model (ERSEM) is one of the most established ecosystem models for the lower trophic levels of the marine food web in the scientific literature. Since its original development in the early nineties it has evolved significantly from a coastal ecosystem model for the North Sea to a generic tool for ecosystem simulations from shelf seas to the global ocean. The current model release contains all essential elements for the pelagic and benthic parts of the marine ecosystem, including the microbial food web, the carbonate system, and calcification. Its distribution is accompanied by a testing framework enabling the analysis of individual parts of the model. Here we provide a detailed mathematical description of all ERSEM components along with case studies of mesocosm-type simulations, water column implementations, and a brief example of a full-scale application for the north-western European shelf. Validation against in situ data demonstrates the capability of the model to represent the marine ecosystem in contrasting environments.

K. S. Siddiqi, Azamal Husen

Nanoscale Research Letters • 2016

Fungi secrete enzymes and proteins as reducing agents which can be used for the synthesis of metal nanoparticles from metal salts. Large-scale production of nanoparticles from diverse fungal strains has great potential since they can be grown even in vitro. In recent years, various approaches have been made to maximize the yield of nanoparticles of varying shape, size, and stability. They have been characterized by thermogravimetric analysis, X-ray diffractometry, SEM/TEM, zeta potential measurements, UV-vis, and Fourier transform infrared (FTIR) spectroscopy. In this review, we focus on the biogenic synthesis of metal nanoparticles by fungi to explore the chemistry of their formation extracellularly and intracellularly. Emphasis has been given to the potential of metal nanoparticles as an antimicrobial agent to inhibit the growth of pathogenic fungi, and on other potential applications.

Wolfgang W. Weisser, Christiane Roscher, Sebastian T. Meyer et al.

Basic and Applied Ecology • 2017

In the past two decades, a large number of studies have investigated the relationship between biodiversity and ecosystem functioning, most of which focussed on a limited set of ecosystem variables. The Jena Experiment was set up in 2002 to investigate the effects of plant diversity on element cycling and trophic interactions, using a multi-disciplinary approach. Here, we review the results of 15 years of research in the Jena Experiment, focussing on the effects of manipulating plant species richness and plant functional richness. With more than 85,000 measures taken from the plant diversity plots, the Jena Experiment has allowed answering fundamental questions important for functional biodiversity research. First, the question was how general the effect of plant species richness is, regarding the many different processes that take place in an ecosystem. About 45% of different types of ecosystem processes measured in the ‘main experiment’, where plant species richness ranged from 1 to 60 species, were significantly affected by plant species richness, providing strong support for the view that biodiversity is a significant driver of ecosystem functioning. Many measures were not saturating at the 60-species level, but increased linearly with the logarithm of species richness. There was, however, great variability in the strength of response among different processes. One striking pattern was that many processes, in particular belowground processes, took several years to respond to the manipulation of plant species richness, showing that biodiversity experiments have to be long-term, to distinguish trends from transitory patterns. In addition, the results from the Jena Experiment provide further evidence that diversity begets stability, for example stability against invasion of plant species, but unexpectedly some results also suggested the opposite, e.g. when plant communities experience severe perturbations or elevated resource availability. This highlights the need to revisit diversity–stability theory. Second, we explored whether individual plant species or individual plant functional groups, or biodiversity itself is more important for ecosystem functioning, in particular biomass production. We found strong effects of individual species and plant functional groups on biomass production, yet these effects mostly occurred in addition to, but not instead of, effects of plant species richness. Third, the Jena Experiment assessed the effect of diversity on multitrophic interactions. The diversity of most organisms responded positively to increases in plant species richness, and the effect was stronger for above- than for belowground organisms, and stronger for herbivores than for carnivores or detritivores. Thus, diversity begets diversity. In addition, the effect on organismic diversity was stronger than the effect on species abundances. Fourth, the Jena Experiment aimed to assess the effect of diversity on N, P and C cycling and the water balance of the plots, separating between element input into the ecosystem, element turnover, element stocks, and output from the ecosystem. While inputs were generally less affected by plant species richness, measures of element stocks, turnover and output were often positively affected by plant diversity, e.g. carbon storage strongly increased with increasing plant species richness. Variables of the N cycle responded less strongly to plant species richness than variables of the C cycle. Fifth, plant traits are often used to unravel mechanisms underlying the biodiversity–ecosystem functioning relationship. In the Jena Experiment, most investigated plant traits, both above- and belowground, were plastic and trait expression depended on plant diversity in a complex way, suggesting limitation to using database traits for linking plant traits to particular functions. Sixth, plant diversity effects on ecosystem processes are often caused by plant diversity effects on species interactions. Analyses i

Aleksandra Checinska Sielaff, Camilla Urbaniak, Ganesh Babu Malli Mohan et al.

Microbiome • 2019

The results reveal a diverse population of bacteria and fungi on ISS environmental surfaces that changed over time but remained similar between locations. The dominant organisms are associated with the human microbiome and may include opportunistic pathogens. This study provides the first comprehensive catalog of both total and intact/viable bacteria and fungi found on surfaces in closed space systems and can be used to help develop safety measures that meet NASA requirements for deep space human habitation. The results of this study can have significant impact on our understanding of other confined built environments on the Earth such as clean rooms used in the pharmaceutical and medical industries.

Paolo Tarolli, Jian Luo, Edward Park et al.

iScience • 2024

Soil salinization is among the most critical threats to agriculture and food security. Excess of salts adversely affects soil structure and fertility, plant growth, crop yield, and microorganisms. It is caused by natural processes, such as dry climates and low precipitations, high evaporation rate, poor waterlogging, and human factors, such as inappropriate irrigation practices, poor drainage systems, and excessive use of fertilizers. The growing extremization of climate with prolonged drought conditions is worsening the phenomenon. Nature-based solutions (NBS), combined with precision or conservation agriculture, represent a sustainable response, and offer benefits through revitalizing ecosystem services. This perspective explores NBS that can be adopted, along with their challenges and implementation limitations. We also argue that NBS could not be enough to combat hunger in the world's most vulnerable regions and fully achieve the Sustainable Development Goal - Zero Hunger (SDG2). We therefore discuss their possible combination with salt-tolerant crops based on bioengineering.

George Zittis, M. Almazroui, Pinhas Alpert et al.

Reviews of Geophysics • 2022

Abstract Observation‐based and modeling studies have identified the Eastern Mediterranean and Middle East (EMME) region as a prominent climate change hotspot. While several initiatives have addressed the impacts of climate change in parts of the EMME, here we present an updated assessment, covering a wide range of timescales, phenomena and future pathways. Our assessment is based on a revised analysis of recent observations and projections and an extensive overview of the recent scientific literature on the causes and effects of regional climate change. Greenhouse gas emissions in the EMME are growing rapidly, surpassing those of the European Union, hence contributing significantly to climate change. Over the past half‐century and especially during recent decades, the EMME has warmed significantly faster than other inhabited regions. At the same time, changes in the hydrological cycle have become evident. The observed recent temperature increase of about 0.45°C per decade is projected to continue, although strong global greenhouse gas emission reductions could moderate this trend. In addition to projected changes in mean climate conditions, we call attention to extreme weather events with potentially disruptive societal impacts. These include the strongly increasing severity and duration of heatwaves, droughts and dust storms, as well as torrential rain events that can trigger flash floods. Our review is complemented by a discussion of atmospheric pollution and land‐use change in the region, including urbanization, desertification and forest fires. Finally, we identify sectors that may be critically affected and formulate adaptation and research recommendations toward greater resilience of the EMME region to climate change.

Jens Terhaar, Ronny Lauerwald, Pierre Regnier et al.

Nature Communications • 2021

Net primary production (NPP) is the foundation of the oceans' ecosystems and the fisheries they support. In the Arctic Ocean, NPP is controlled by a complex interplay of light and nutrients supplied by upwelling as well as lateral inflows from adjacent oceans and land. But so far, the role of the input from land by rivers and coastal erosion has not been given much attention. Here, by upscaling observations from the six largest rivers and using measured coastal erosion rates, we construct a pan-Arctic, spatio-temporally resolved estimate of the land input of carbon and nutrients to the Arctic Ocean. Using an ocean-biogeochemical model, we estimate that this input fuels 28-51% of the current annual Arctic Ocean NPP. This strong enhancement of NPP is a consequence of efficient recycling of the land-derived nutrients on the vast Arctic shelves. Our results thus suggest that nutrient input from the land is a key process that will affect the future evolution of Arctic Ocean NPP.

Nicole Boivin, Melinda A. Zeder, Dorian Q. Fuller et al.

Proceedings of the National Academy of Sciences • 2016

The exhibition of increasingly intensive and complex niche construction behaviors through time is a key feature of human evolution, culminating in the advanced capacity for ecosystem engineering exhibited by Homo sapiens A crucial outcome of such behaviors has been the dramatic reshaping of the global biosphere, a transformation whose early origins are increasingly apparent from cumulative archaeological and paleoecological datasets. Such data suggest that, by the Late Pleistocene, humans had begun to engage in activities that have led to alterations in the distributions of a vast array of species across most, if not all, taxonomic groups. Changes to biodiversity have included extinctions, extirpations, and shifts in species composition, diversity, and community structure. We outline key examples of these changes, highlighting findings from the study of new datasets, like ancient DNA (aDNA), stable isotopes, and microfossils, as well as the application of new statistical and computational methods to datasets that have accumulated significantly in recent decades. We focus on four major phases that witnessed broad anthropogenic alterations to biodiversity-the Late Pleistocene global human expansion, the Neolithic spread of agriculture, the era of island colonization, and the emergence of early urbanized societies and commercial networks. Archaeological evidence documents millennia of anthropogenic transformations that have created novel ecosystems around the world. This record has implications for ecological and evolutionary research, conservation strategies, and the maintenance of ecosystem services, pointing to a significant need for broader cross-disciplinary engagement between archaeology and the biological and environmental sciences.

Rebecca A. Daly, Mikayla Borton, Michael J. Wilkins et al.

Nature Microbiology • 2016

Hydraulic fracturing is the industry standard for extracting hydrocarbons from shale formations. Attention has been paid to the economic benefits and environmental impacts of this process, yet the biogeochemical changes induced in the deep subsurface are poorly understood. Recent single-gene investigations revealed that halotolerant microbial communities were enriched after hydraulic fracturing. Here, the reconstruction of 31 unique genomes coupled to metabolite data from the Marcellus and Utica shales revealed that many of the persisting organisms play roles in methylamine cycling, ultimately supporting methanogenesis in the deep biosphere. Fermentation of injected chemical additives also sustains long-term microbial persistence, while thiosulfate reduction could produce sulfide, contributing to reservoir souring and infrastructure corrosion. Extensive links between viruses and microbial hosts demonstrate active viral predation, which may contribute to the release of labile cellular constituents into the extracellular environment. Our analyses show that hydraulic fracturing provides the organismal and chemical inputs for colonization and persistence in the deep terrestrial subsurface.

Jianchao Zhang, Yahai Lu

Frontiers in Microbiology • 2016

Syntrophic methanogenesis is an essential link in the global carbon cycle and a key bioprocess for the disposal of organic waste and production of biogas. Recent studies suggest direct interspecies electron transfer (DIET) is involved in electron exchange in methanogenesis occurring in paddy soils, anaerobic digesters, and specific co-cultures with Geobacter. In this study, we evaluate the possible involvement of DIET in the syntrophic oxidation of butyrate in the enrichments from two lake sediments (an urban lake and a natural lake). The results showed that the production of CH4 was significantly accelerated in the presence of conductive nanoscale Fe3O4 or carbon nanotubes in the sediment enrichments. Observations made with fluorescence in situ hybridization and scanning electron microscope indicated that microbial aggregates were formed in the enrichments. It appeared that the average cell-to-cell distance in aggregates in nanomaterial-amended enrichments was larger than that in aggregates in the non-amended control. These results suggested that DIET-mediated syntrophic methanogenesis could occur in the lake sediments in the presence of conductive materials. Microbial community analysis of the enrichments revealed that the genera of Syntrophomonas, Sulfurospirillum, Methanosarcina, and Methanoregula were responsible for syntrophic oxidation of butyrate in lake sediment samples. The mechanism for the conductive-material-facilitated DIET in butyrate syntrophy deserves further investigation.

P. N. Obasi, Bennard Benedict Akudinobi

Applied Water Science • 2020

Abstract Heavy metals are potential health risk, especially in mining sites where they deteriorate from sulfide-rich ore bodies. Lead, cadmium, arsenic and mercury are very carcinogenic, while others are toxic. The assessment of the levels of these metals in water resources of the lead–zinc mining communities of Enyigba, Mkpuma Akpatakpa, Ameka, Amorie, Amanchara and Alibaruhu was carried out, and the potential health risk has been investigated. These areas make up the main mining communities of Abakaliki, where active and abandoned mines are located. One hundred and six water samples were analyzed in two seasons using atomic absorption spectrophotometric and ultra-violet/visible spectroscopy. Result indicates levels of Pb 2+ > Hg 2+ > As 2+ > Cd 2+ > Mn 2+ > Ag 2+ > Se 2+ > Ni 2+ > Cr 2+ > Cu 2+ in water sources. High levels of Mn 2+ (63.45 mg/L), Pb 2+ (11.42 mg/L), Cr 3+ (14.60 mg/L), Ni 2+ (1.260), Cd 2+ (15.67 mg/L), Ag + (6.06 mg/L), Hg 2+ (2.60 mg/L), As(4.13 mg/L), Se 2+ (2.68 mg/L), Zn 2+ (10.53 mg/L) and Co 2+ (0.9 mg/L) above the WHO recommended standard for drinking water were observed. Only Cu 2+ recorded safe concentrations in 100% samples analyzed. Levels of associated metals including Pb 2+ , As, Hg 2+ , Se 2+ and Cd 2+ are higher in groundwater especially in areas close to the active mines; this is due to mineralization in the area. Seasonal analysis shows a decreased concentration of chemical constituents in the rainy season relative to the dry season. Potential health risk is associated with accumulation of toxic heavy metals in tissues including Parkinson disease, arsenicosis, acrodynia, selenoises, Alzheimer’s disease, hair loss, mental imbalance and abortion in women abound in the areas. Alternative water supply sources and sensitization on the potential health risk are highly advocated in these communities.

Vivek K. Arora, Anna Katavouta, Richard G. Williams et al.

Biogeosciences • 2020

Abstract. Results from the fully and biogeochemically coupled simulations in which CO2 increases at a rate of 1 % yr−1 (1pctCO2) from its preindustrial value are analyzed to quantify the magnitude of carbon–concentration and carbon–climate feedback parameters which measure the response of ocean and terrestrial carbon pools to changes in atmospheric CO2 concentration and the resulting change in global climate, respectively. The results are based on 11 comprehensive Earth system models from the most recent (sixth) Coupled Model Intercomparison Project (CMIP6) and compared with eight models from the fifth CMIP (CMIP5). The strength of the carbon–concentration feedback is of comparable magnitudes over land (mean ± standard deviation = 0.97 ± 0.40 PgC ppm−1) and ocean (0.79 ± 0.07 PgC ppm−1), while the carbon–climate feedback over land (−45.1 ± 50.6 PgC ∘C−1) is about 3 times larger than over ocean (−17.2 ± 5.0 PgC ∘C−1). The strength of both feedbacks is an order of magnitude more uncertain over land than over ocean as has been seen in existing studies. These values and their spread from 11 CMIP6 models have not changed significantly compared to CMIP5 models. The absolute values of feedback parameters are lower for land with models that include a representation of nitrogen cycle. The transient climate response to cumulative emissions (TCRE) from the 11 CMIP6 models considered here is 1.77 ± 0.37 ∘C EgC−1 and is similar to that found in CMIP5 models (1.63 ± 0.48 ∘C EgC−1) but with somewhat reduced model spread. The expressions for feedback parameters based on the fully and biogeochemically coupled configurations of the 1pctCO2 simulation are simplified when the small temperature change in the biogeochemically coupled simulation is ignored. Decomposition of the terms of these simplified expressions for the feedback parameters is used to gain insight into the reasons for differing responses among ocean and land carbon cycle models.

Hans Peter H. Arp, Dana Kühnel, Christoph Rummel et al.

Environmental Science & Technology • 2021

We described in 2017 how weathering plastic litter in the marine environment fulfils two of three criteria to impose a planetary boundary threat related to "chemical pollution and the release of novel entities": (1) planetary-scale exposure, which (2) is not readily reversible. Whether marine plastics meet the third criterion, (3) eliciting a disruptive impact on vital earth system processes, was uncertain. Since then, several important discoveries have been made to motivate a re-evaluation. A key issue is if weathering macroplastics, microplastics, nanoplastics, and their leachates have an inherently higher potential to elicit adverse effects than natural particles of the same size. We summarize novel findings related to weathering plastic in the context of the planetary boundary threat criteria that demonstrate (1) increasing exposure , (2) fate processes leading to poorly reversible pollution, and (3) (eco)toxicological hazards and their thresholds. We provide evidence that the third criterion could be fulfilled for weathering plastics in sensitive environments and therefore conclude that weathering plastics pose a planetary boundary threat. We suggest future research priorities to better understand (eco)toxicological hazards modulated by increasing exposure and continuous weathering processes, to better parametrize the planetary boundary threshold for plastic pollution.

Sascha Krause, Timothy A. Johnson, Yasodara Samadhi Karunaratne et al.

Proceedings of the National Academy of Sciences • 2016

The utilization of methane, a potent greenhouse gas, is an important component of local and global carbon cycles that is characterized by tight linkages between methane-utilizing (methanotrophic) and nonmethanotrophic bacteria. It has been suggested that the methanotroph sustains these nonmethanotrophs by cross-feeding, because subsequent products of the methane oxidation pathway, such as methanol, represent alternative carbon sources. We established cocultures in a microcosm model system to determine the mechanism and substrate that underlay the observed cross-feeding in the environment. Lanthanum, a rare earth element, was applied because of its increasing importance in methylotrophy. We used co-occurring strains isolated from Lake Washington sediment that are involved in methane utilization: a methanotroph and two nonmethanotrophic methylotrophs. Gene-expression profiles and mutant analyses suggest that methanol is the dominant carbon and energy source the methanotroph provides to support growth of the nonmethanotrophs. However, in the presence of the nonmethanotroph, gene expression of the dominant methanol dehydrogenase (MDH) shifts from the lanthanide-dependent MDH (XoxF)-type, to the calcium-dependent MDH (MxaF)-type. Correspondingly, methanol is released into the medium only when the methanotroph expresses the MxaF-type MDH. These results suggest a cross-feeding mechanism in which the nonmethanotrophic partner induces a change in expression of methanotroph MDHs, resulting in release of methanol for its growth. This partner-induced change in gene expression that benefits the partner is a paradigm for microbial interactions that cannot be observed in studies of pure cultures, underscoring the importance of synthetic microbial community approaches to understand environmental microbiomes.

James E. Hansen, Makiko Sato, Paul J. Hearty et al.

Atmospheric chemistry and physics • 2016

Abstract. We use numerical climate simulations, paleoclimate data, and modern observations to study the effect of growing ice melt from Antarctica and Greenland. Meltwater tends to stabilize the ocean column, inducing amplifying feedbacks that increase subsurface ocean warming and ice shelf melting. Cold meltwater and induced dynamical effects cause ocean surface cooling in the Southern Ocean and North Atlantic, thus increasing Earth's energy imbalance and heat flux into most of the global ocean's surface. Southern Ocean surface cooling, while lower latitudes are warming, increases precipitation on the Southern Ocean, increasing ocean stratification, slowing deepwater formation, and increasing ice sheet mass loss. These feedbacks make ice sheets in contact with the ocean vulnerable to accelerating disintegration. We hypothesize that ice mass loss from the most vulnerable ice, sufficient to raise sea level several meters, is better approximated as exponential than by a more linear response. Doubling times of 10, 20 or 40 years yield multi-meter sea level rise in about 50, 100 or 200 years. Recent ice melt doubling times are near the lower end of the 10–40-year range, but the record is too short to confirm the nature of the response. The feedbacks, including subsurface ocean warming, help explain paleoclimate data and point to a dominant Southern Ocean role in controlling atmospheric CO2, which in turn exercised tight control on global temperature and sea level. The millennial (500–2000-year) timescale of deep-ocean ventilation affects the timescale for natural CO2 change and thus the timescale for paleo-global climate, ice sheet, and sea level changes, but this paleo-millennial timescale should not be misinterpreted as the timescale for ice sheet response to a rapid, large, human-made climate forcing. These climate feedbacks aid interpretation of events late in the prior interglacial, when sea level rose to +6–9 m with evidence of extreme storms while Earth was less than 1 °C warmer than today. Ice melt cooling of the North Atlantic and Southern oceans increases atmospheric temperature gradients, eddy kinetic energy and baroclinicity, thus driving more powerful storms. The modeling, paleoclimate evidence, and ongoing observations together imply that 2 °C global warming above the preindustrial level could be dangerous. Continued high fossil fuel emissions this century are predicted to yield (1) cooling of the Southern Ocean, especially in the Western Hemisphere; (2) slowing of the Southern Ocean overturning circulation, warming of the ice shelves, and growing ice sheet mass loss; (3) slowdown and eventual shutdown of the Atlantic overturning circulation with cooling of the North Atlantic region; (4) increasingly powerful storms; and (5) nonlinearly growing sea level rise, reaching several meters over a timescale of 50–150 years. These predictions, especially the cooling in the Southern Ocean and North Atlantic with markedly reduced warming or even cooling in Europe, differ fundamentally from existing climate change assessments. We discuss observations and modeling studies needed to refute or clarify these assertions.

Kwame Ampong, Malinda S. Thilakaranthna, Linda Yuya Gorim

Frontiers in Agronomy • 2022

Humic acids (HA) are organic molecules that play essential roles in improving soil properties, plant growth, and agronomic parameters. The sources of HA include coal, lignite, soils, and organic materials. Humic acid-based products have been used in crop production in recent years to ensure the sustainability of agriculture production. Reviewed literature shows that HA can positively affect soil physical, chemical, and biological characteristics, including texture, structure, water holding capacity, cation exchange capacity, pH, soil carbon, enzymes, nitrogen cycling, and nutrient availability. This review highlights the relevance of HA on crop growth, plant hormone production, nutrient uptake and assimilation, yield, and protein synthesis. The effect of HA on soil properties and crops is influenced by the HA type, HA application rate, HA application mode, soil type, solubility, molecular size, and functional group. This review also identifies some knowledge gaps in HA studies. HA and its application rate have not been tested in field experiments under different crops in rotation, nitrogen fertilizer forms, sites and climatic conditions. Furthermore, HA chemical and molecular structures, their water and alkaline soluble fractions have not been tested under field experiments to evaluate their effects on crop yield, quality, and soil health. The relationship between soil-plant nutrient availability and plant nutrient uptake following HA application should also be further studied.

Katey Walter Anthony, Thomas Schneider von Deimling, Ingmar Nitze et al.

Nature Communications • 2018

Permafrost carbon feedback (PCF) modeling has focused on gradual thaw of near-surface permafrost leading to enhanced carbon dioxide and methane emissions that accelerate global climate warming. These state-of-the-art land models have yet to incorporate deeper, abrupt thaw in the PCF. Here we use model data, supported by field observations, radiocarbon dating, and remote sensing, to show that methane and carbon dioxide emissions from abrupt thaw beneath thermokarst lakes will more than double radiative forcing from circumpolar permafrost-soil carbon fluxes this century. Abrupt thaw lake emissions are similar under moderate and high representative concentration pathways (RCP4.5 and RCP8.5), but their relative contribution to the PCF is much larger under the moderate warming scenario. Abrupt thaw accelerates mobilization of deeply frozen, ancient carbon, increasing 14 C-depleted permafrost soil carbon emissions by ~125-190% compared to gradual thaw alone. These findings demonstrate the need to incorporate abrupt thaw processes in earth system models for more comprehensive projection of the PCF this century.

Daniel Schlatter, Linda L. Kinkel, Linda S. Thomashow et al.

Phytopathology • 2017

Soils suppressive to soilborne pathogens have been identified worldwide for almost 60 years and attributed mainly to suppressive or antagonistic microorganisms. Rather than identifying, testing and applying potential biocontrol agents in an inundative fashion, research into suppressive soils has attempted to understand how indigenous microbiomes can reduce disease, even in the presence of the pathogen, susceptible host, and favorable environment. Recent advances in next-generation sequencing of microbiomes have provided new tools to reexamine and further characterize the nature of these soils. Two general types of suppression have been described: specific and general suppression, and theories have been developed around these two models. In this review, we will present three examples of currently-studied model systems with features representative of specific and general suppressiveness: suppression to take-all (Gaeumannomyces graminis var. tritici), Rhizoctonia bare patch of wheat (Rhizoctonia solani AG-8), and Streptomyces. To compare and contrast the two models of general versus specific suppression, we propose a number of hypotheses about the nature and ecology of microbial populations and communities of suppressive soils. We outline the potential and limitations of new molecular techniques that can provide novel ways of testing these hypotheses. Finally, we consider how this greater understanding of the phytobiome can facilitate sustainable disease management in agriculture by harnessing the potential of indigenous soil microbes.

Kaustuvmani Patowary, Rupshikha Patowary, Mohan Chandra Kalita et al.

Frontiers in Microbiology • 2017

Production and spillage of petroleum hydrocarbons which is the most versatile energy resource causes disastrous environmental pollution. Elevated oil degrading performance from microorganisms is demanded for successful microbial remediation of those toxic pollutants. The employment of biosurfactant-producing and hydrocarbon-utilizing microbes enhances the effectiveness of bioremediation as biosurfactant plays a key role by making hydrocarbons bio-available for degradation. The present study aimed the isolation of a potent biosurfactant producing indigenous bacteria which can be employed for crude oil remediation, along with the characterization of the biosurfactant produced during crude oil biodegradation. A potent bacterial strain Pseudomonas aeruginosa PG1 (identified by 16s rDNA sequencing) was isolated from hydrocarbon contaminated soil that could efficiently produce biosurfactant by utilizing crude oil components as the carbon source, thereby leading to the enhanced degradation of the petroleum hydrocarbons. Strain PG1 could degrade 81.8% of total petroleum hydrocarbons (TPH) after 5 weeks of culture when grown in mineral salt media (MSM) supplemented with 2% (v/v) crude oil as the sole carbon source. GCMS analysis of the treated crude oil samples revealed that P. aeruginosa PG1 could potentially degrade various hydrocarbon contents including various PAHs present in the crude oil. Biosurfactant produced by strain PG1 in the course of crude oil degradation, promotes the reduction of surface tension (ST) of the culture medium from 51.8 to 29.6 mN m -1 , with the critical micelle concentration (CMC) of 56 mg L -1 . FTIR, LC-MS, and SEM-EDS studies revealed that the biosurfactant is a rhamnolipid comprising of both mono and di rhamnolipid congeners. The biosurfactant did not exhibit any cytotoxic effect to mouse L292 fibroblastic cell line, however, strong antibiotic activity against some pathogenic bacteria and fungus was observed.

Gessesse Kebede Bekele, Tekle Tafese, Ebrahim M. Abda et al.

Journal of Chemistry • 2021

The discharge of hydrocarbons and their derivatives to environments due to human and/or natural activities cause environmental pollution (soil, water, and air) and affect the natural functioning of an ecosystem. To minimize or eradicate environmental pollution by hydrocarbon contaminants, studies showed strategies including physical, chemical, and biological approaches. Among those strategies, the use of biological techniques (especially bacterial biodegradation) is critically important to remove hydrocarbon contaminants. The current review discusses the insights of major factors that enhance or hinder the bacterial bioremediation of hydrocarbon contaminants (aliphatic, aromatic, and polyaromatic hydrocarbons) in the soil. The key factors limiting the overall hydrocarbon biodegradation are generally categorized as biotic factors and abiotic factors. Among various environmental factors, temperature range from 30 to 40°C, pH range from 5 to 8, moisture availability range from 30 to 90%, carbon/nitrogen/phosphorous (C/N/P; 100:20:1) ratio, and 10–40% of oxygen for aerobic degradation are the key factors that show positive correlation for greatest hydrocarbon biodegradation rate by altering the activities of the microbial and degradative enzymes in soil. In addition, the formation of biofilm and production of biosurfactants in hydrocarbon-polluted soil environments increase microbial adaptation to low bioavailability of hydrophobic compounds, and genes that encode for hydrocarbon degradative enzymes are critical for the potential of microbes to bioremediate soils contaminated with hydrocarbon pollutants. Therefore, this review works on the identification of factors for effective hydrocarbon biodegradation, understanding, and optimization of those factors that are essential and critical.

Baogang Zhang, Song Wang, Muhe Diao et al.

Journal of Geophysical Research Biogeosciences • 2019

Abstract Vanadium mining activities can cause contamination of the surrounding geological environment. Vanadium may exist in multiple matrices due to its migration and transformation, forming interactive relationships; however, the connection between vanadium distributions in multiple matrices and microbial community responses remains largely unknown. Vanadium is a redox‐sensitive metal that can be microbiologically reduced and immobilized. To date, bioremediation of vanadium‐contaminated environments by indigenous microorganisms has rarely been evaluated. This paper reports a systematic investigation into vanadium distributions and microbial communities in soils, water, and sediment from Panzhihua, China. Large vanadium contents of 1130.1 ± 9.8 mg/kg and 0.13 ± 0.02 mg/L were found in surface soil and groundwater. Vanadium in surface water tended to precipitate. Microbial communities isolated from similar environments were alike due to similarity in matrix chemistry whereas communities were distinct when compared to different matrices, with lower richness and diversity in groundwater. Proteobacteria was distributed widely and dominated microbial communities within groundwater. Redundancy analysis shows that vanadium and nutrients significantly affected metal‐tolerant bacteria. Long‐term cultivation (240 days) suggests the possibility of vanadium bioremediation by indigenous microorganisms, within acid‐soluble fraction. This active fraction can potentially release mobile vanadium with shifted redox conditions. Vanadium (V) was bio‐reduced to less toxic, mobile vanadium (IV) primarily by enriched Bacillus and Thauera . This study reveals the biogeochemical fate of vanadium in regional geological environments and suggests a bioremediation pathway via native vanadium‐reducing microbes.

Tony Yang, Kadambot H. M. Siddique, Kui Liu

Global Ecology and Conservation • 2020

Soil health is defined as the capacity of soil to function, within ecosystem boundaries, to sustain crop and animal productivities, maintain or enhance environmental sustainability, and improve human health worldwide. In agro-ecosystems, the soil health can change due to anthropogenic activities, such as preferred cropping practices and intensive land-use management, which can further impact soil functions. Previous assessment of soil health in agriculture mostly relates to soil eco-functions that are integrated with non-biological properties such as soil nutrients and soil structures. In recent years, biological properties such as soil microorganisms were considered as an essential composition in soil health as well. However, systematic reviews of soil health and its potential feedback to human society under different cropping practices are still limited. In this review, we discussed 1) the impact of common and novel cropping practices in agro-systems on soil health, 2) the evolution of plant–microbe–soil complex and the biochemical mechanisms under the pressure of agriculture that responsible for soil health, 3) changes in the concept of soil quality and health over recent decades in agro-systems and the key indicators currently used for evaluating soil health, and 4) issues in agroecosystems that affect soil health the most, particularly how various cropping practices have developed over time with human activities in agroecosystem. This knowledge, along with necessary policies, will help to ensure healthy soil—a crucial component for sustainable ecosystem development.

Melania E. Cristescu, Paul D. N. Hebert

Annual Review of Ecology Evolution and Systematics • 2018

The study of environmental DNA (eDNA) has the potential to revolutionize biodiversity science and conservation action by enabling the census of species on a global scale in near real time. To achieve this promise, technical challenges must be resolved. In this review, we explore the main uses of eDNA as well as the complexities introduced by its misuse. Current eDNA methods require refinement and improved calibration and validation along the entire workflow to lessen false positives/negatives. Moreover, there is great need for a better understanding of the “natural history” of eDNA—its origins, state, lifetime, and transportation—and for more detailed insights concerning the physical and ecological limitations of eDNA use. Although eDNA analysis can provide powerful information, particularly in freshwater and marine environments, its impact is likely to be less significant in terrestrial settings. The broad adoption of eDNA tools in conservation will largely depend on addressing current uncertainties in data interpretation.

David W. Waite, Inka Vanwonterghem, Christian Rinke et al.

Frontiers in Microbiology • 2017

The Epsilonproteobacteria is the fifth validly described class of the phylum Proteobacteria, known primarily for clinical relevance and for chemolithotrophy in various terrestrial and marine environments, including deep-sea hydrothermal vents. As 16S rRNA gene repositories have expanded and protein marker analysis become more common, the phylogenetic placement of this class has become less certain. A number of recent analyses of the bacterial tree of life using both 16S rRNA and concatenated marker gene analyses have failed to recover the Epsilonproteobacteria as monophyletic with all other classes of Proteobacteria. In order to address this issue, we investigated the phylogenetic placement of this class in the bacterial domain using 16S and 23S rRNA genes, as well as 120 single-copy marker proteins. Single- and concatenated-marker trees were created using a data set of 4,170 bacterial representatives, including 98 Epsilonproteobacteria . Phylogenies were inferred under a variety of tree building methods, with sequential jackknifing of outgroup phyla to ensure robustness of phylogenetic affiliations under differing combinations of bacterial genomes. Based on the assessment of nearly 300 phylogenetic tree topologies, we conclude that the continued inclusion of Epsilonproteobacteria within the Proteobacteria is not warranted, and that this group should be reassigned to a novel phylum for which we propose the name Epsilonbacteraeota (phyl. nov.). We further recommend the reclassification of the order Desulfurellales ( Deltaproteobacteria ) to a novel class within this phylum and a number of subordinate changes to ensure consistency with the genome-based phylogeny. Phylogenomic analysis of 658 genomes belonging to the newly proposed Epsilonbacteraeota suggests that the ancestor of this phylum was an autotrophic, motile, thermophilic chemolithotroph that likely assimilated nitrogen from ammonium taken up from the environment or generated from environmental nitrate and nitrite by employing a variety of functional redox modules. The emergence of chemoorganoheterotrophic lifestyles in several Epsilonbacteraeota families is the result of multiple independent losses of various ancestral chemolithoautotrophic pathways. Our proposed reclassification of this group resolves an important anomaly in bacterial systematics and ensures that the taxonomy of Proteobacteria remains robust, specifically as genome-based taxonomies become more common.