Waheed Miran, Jiseon Jang, Mohsin Nawaz et al.

Chemosphere • 2017

Waheed Miran, Mohsin Nawaz, Jiseon Jang et al.

The Science of The Total Environment • 2016

Lu Wang, Le-Xing You, Jiaming Zhang et al.

Journal of Hazardous Materials • 2018

Hai–Liang Song, Hua Li, Shuai Zhang et al.

Chemical Engineering Journal • 2018

Junfeng Wang, Xinshan Song, Yuhui Wang et al.

The Science of The Total Environment • 2017

Hua Li, Han Xu, Yu-Li Yang et al.

Water Research • 2019

Young-Hyun Park, Seonghwan Park, Văn Khánh Nguyễn et al.

Chemical Engineering Journal • 2017

Waheed Miran, Jiseon Jang, Mohsin Nawaz et al.

The Science of The Total Environment • 2018

Tian Xia, Xueli Zhang, Huimin Wang et al.

Bioresource Technology • 2019

Yining Wu, Xin Zhao, Min Jin et al.

Bioresource Technology • 2018

I.G. Ezemagu, Marcel I. Ejimofor, Matthew C. Menkiti et al.

South African Journal of Chemical Engineering • 2020

In this study, results of parametric effects and optimization of turbidity removal from produced water using response surface methodology (RSM) and artificial neural network (ANN) based on a statistically designed experimentation via the Box–Behnken design (BBD) are reported. A three-level, three-factor BBD was employed using dosage (x1), time (x2) and temperature (x3) as process variables. A quadratic polynomial model was obtained to predict turbidity removal efficiency. The RSM model predicted an optimal turbidity removal efficiency of 83% at conditions of x1 (1 g/L), x2 (16.5 min) and x3 (45 °C) and validated experimentally as 82.73% with low model lack of fit F value of 0.6 and CV value of 8.22%. The ANN model predicted optimal turbidity removal of 83.01% at conditions of x1 (1 g/L), x2 (16.5 min) and x3 (45 °C) and validated as 82.98%. Both models showed to be effective in describing the parametric effect of the considered operating variables on the turbidity removal from produced water. However, the ANN described the parametric effect more accurately when compared with the RSM model, with a smaller PRE (percentage relative error) and AAD (absolute average deviation) of ±0.0241% and ±0.0139%, respectively.

Chao Zhang, Rui Yang, Meichen Sun et al.

Biochar • 2022

Abstract Anaerobic digestion (AD) has been considered as a promising technique for food waste (FW) recycling. However, the accumulation of volatile fatty acids (VFAs) restricts the stability of anaerobic reactors. The present study investigated the use of biochar produced at different conditions (750 °C-30 min, 750 °C-60 min, 750 °C-120 min, 550 °C-60 min, 650 °C-60 min, 850 °C-60 min, 950 °C-60 min) for enhancing the AD of FW. Batch experiments showed that all the biochar increased the methane production rates and biochar obtained at 750 °C-60 min resulted in the highest enhancement by 21.5%. It was further showed surface oxygen-containing functional groups and graphitization degree of biochar were the critical factors for improving methane production. Microbial analysis showed that biochar addition formed different microbial communities, and Methanosaeta , Romboutsia , and norank_f_Anaerolineaceae were enriched, which might be correlated with direct interspecies electron transfer (DIET). This research showed biochar could enhance the AD of FW and also revealed the main characteristics of biochar relating with the enhancement of AD. Graphical Abstract

Kefang He, Ying Liu, Longjin Tian et al.

Heliyon • 2024

Due to the special property of food waste (FW), anaerobic digestion of food waste is facing many challenges like foaming, acidification, ammonia nitrogen and (NH 4 + -N) inhibition which resulted in a low biogas yield. A better understanding on the problems exiting in the FW anaerobic digestion would enhance the bio-energy recovery and increase the stable operation. Meanwhile, to overcome the bottle necks, pretreatment, co-digestion and additives is proposed as well as the solutions to improve biogas yield in FW digestion system. At last, future research directions regarding FW anaerobic digestion were proposed.

Yimeng Zhang, Xiaofan Zhai, Fang Guan et al.

npj Materials Degradation • 2022

Abstract Petroleum-hydrocarbons spilt in surface seawater may pose potential threats to the corrosion of steel infrastructures. We show that crude oil accelerated steel corrosion mainly by accelerating microbiologically influenced corrosion (MIC). Crude oil led to the dominance of marine oil-degraders including Alcanivorax and Marinobacter in both seawater and steel rust, rather than sulfate-reducing bacteria (SRB) which dominated the rust microbial community in the no-oil group. Crude oil not only enhanced microbial oxygen respiration and aerobic hydrocarbon degradation but also nitrate reduction and anaerobic hydrocarbon degradation process in steel rust, indicating more heterogeneous microenvironments formed on steel surfaces. Furthermore, the low abundance of SRB and dissimilatory sulfate reduction gene ( dsr ), and the existence of iron-carbonate and iron-sulfate minerals implied that microbial sulfide, previously regarded as the main cause of MIC, was not the major contributor to steel corrosion in early petroleum-polluted seawater. Marine specialized oil-degraders seem to play more significant roles under such conditions.

Maria da Glória C. Silva, Anderson O. de Medeiros, Attílio Converti et al.

Sustainability • 2024

Population growth and the need for increased agricultural productivity pose a global problem. Therefore, the development of green compounds to ensure agricultural sustainability is an urgent necessity. Surfactant compounds hold significant commercial importance due to their diverse industrial uses. However, the synthetic origin of these agents limits their commercial application due to their toxicity. As a result, extensive research has focused on the production of microbial-originated green surfactants, known as biosurfactants, over the past fifteen years. These biomolecules not only offer a green alternative for agriculture but also exhibit reduced toxicity and excellent stability under specific environmental conditions. Biosurfactants can lower surface tension more effectively than synthetic surfactants. With properties such as detergency and foam formation, biosurfactants are suitable for various agricultural applications, particularly in pesticide and agrochemical formulations. They can function as biopesticides to manage pests, pathogens, phytopathogenic fungi, and weeds due to their antimicrobial activity. Moreover, plants can benefit from biosurfactant molecules and microorganisms as nutrients. They can also aid efficiently in the distribution of micronutrients and metals in the soil. They also stimulate plant immunity and are utilized for soil hydrophilization to ensure proper moisture levels and uniform fertilizer distribution. This review aims to provide valuable insights into the role and properties of biosurfactants as agricultural adjuvants, fostering the development of sustainable formulations to replace the chemical surfactants used in pesticides. For this purpose, the general aspects of global agricultural activity are initially described, followed by a discussion of pesticides, including herbicides, fungicides, and insecticide products. Next, the properties of chemical surfactants are discussed and the use of green surfactants, with emphasis on microbial biosurfactants, is demonstrated. The application of biosurfactants in the agricultural industry and trends are addressed and prospects for the application of these agents are discussed.

John F. Stolz

FEMS Microbiology Ecology • 2016

The Gaia hypothesis, proposed 50 years ago, posits that the Earth's biosphere, atmosphere, hydrosphere and lithosphere interact as a cybernetic system, maintaining the long-term habitability of the planet. The resulting chemical composition of the atmosphere, oceans and crust is unique as compared to the other planets of our solar system, and due to the presence of life. Together these components comprise the biosphere, the life support system of the planet, with most of the essential processes carried out by microbes. Over a half of the elements in the periodic table are now known to have some biological role with many having complex biogeochemical cycles. The global microbiome inhabits a wide range of environments including deep into the Earth's crust, with a population of ∼10 30 cells and more than a trillion species. Deep sequencing projects have revealed hitherto unknown phyla and 'microbial dark matter'. The discoveries of conductive pili and cable bacteria have demonstrated that microbes transfer electrons to and from external sources, sometimes over significant distances, while research on quorum sensing and the plethora of microbial volatile organic substances have provided new insights into how microbes communicate. These advances in microbiology have expanded our understanding how Gaia could actually work.

Roey Angel, Ralf Conrad, Miroslav Dvorský et al.

Microbial Ecology • 2016

Upward migration of plants to barren subnival areas is occurring worldwide due to raising ambient temperatures and glacial recession. In summer 2012, the presence of six vascular plants, growing in a single patch, was recorded at an unprecedented elevation of 6150 m.a.s.l. close to the summit of Mount Shukule II in the Western Himalayas (Ladakh, India). Whilst showing multiple signs of stress, all plants have managed to establish stable growth and persist for several years. To learn about the role of microbes in the process of plant upward migration, we analysed the root-associated microbial community of the plants (three individuals from each) using microscopy and tagged amplicon sequencing. No mycorrhizae were found on the roots, implying they are of little importance to the establishment and early growth of the plants. However, all roots were associated with a complex bacterial community, with richness and diversity estimates similar or even higher than the surrounding bare soil. Both soil and root-associated communities were dominated by members of the orders Sphingomonadales and Sphingobacteriales, which are typical for hot desert soils, but were different from communities of temperate subnival soils and typical rhizosphere communities. Despite taxonomic similarity on the order level, the plants harboured a unique set of highly dominant operational taxonomic units which were not found in the bare soil. These bacteria have been likely transported with the dispersing seeds and became part of the root-associated community following germination. The results indicate that developing soils act not only as a source of inoculation to plant roots but also possibly as a sink for plant-associated bacteria.

Davide Francioli, Geeisy Cid, Saranya Kanukollu et al.

Frontiers in Microbiology • 2021

Flooding affects both above- and below-ground ecosystem processes, and it represents a substantial threat for crop and cereal productivity under climate change. Plant-associated microbiota play a crucial role in plant growth and fitness, but we still have a limited understanding of the response of the crop-microbiota complex under extreme weather events, such as flooding. Soil microbes are highly sensitive to abiotic disturbance, and shifts in microbial community composition, structure and functions are expected when soil conditions are altered due to flooding events (e.g., anoxia, pH alteration, changes in nutrient concentration). Here, we established a pot experiment to determine the effects of flooding stress on the spring wheat-microbiota complex. Since plant phenology could be an important factor in the response to hydrological stress, flooding was induced only once and at different plant growth stages (PGSs), such as tillering, booting and flowering. After each flooding event, we measured in the control and flooded pots several edaphic and plant properties and characterized the bacterial community associated to the rhizosphere and roots of wheat plant using a metabarcoding approach. In our study, flooding caused a significant reduction in plant development and we observed dramatic shifts in bacterial community composition at each PGS in which the hydrological stress was induced. However, a more pronounced disruption in community assembly was always shown in younger plants. Generally, flooding caused a (i) significant increase of bacterial taxa with anaerobic respiratory capabilities, such as members of Firmicutes and Desulfobacterota, (ii) a significant reduction in Actinobacteria and Proteobacteria, (iii) depletion of several putative plant-beneficial taxa, and (iv) increases of the abundance of potential detrimental bacteria. These significant differences in community composition between flooded and control samples were correlated with changes in soil conditions and plant properties caused by the hydrological stress, with pH and total N as the soil, and S, Na, Mn, and Ca concentrations as the root properties most influencing microbial assemblage in the wheat mircobiota under flooding stress. Collectively, our findings demonstrated the role of flooding on restructuring the spring wheat microbiota, and highlighted the detrimental effect of this hydrological stress on plant fitness and performance.

Mateusz Łężyk, Carsten Jers, Louise Kjærulff et al.

PLoS ONE • 2016

This paper describes the discovery of novel α-L-fucosidases and evaluation of their potential to catalyse the transglycosylation reaction leading to production of fucosylated human milk oligosaccharides. Seven novel α-L-fucosidase-encoding genes were identified by functional screening of a soil-derived metagenome library and expressed in E. coli as recombinant 6xHis-tagged proteins. All seven fucosidases belong to glycosyl hydrolase family 29 (GH 29). Six of the seven α-L-fucosidases were substrate-inhibited, moderately thermostable and most hydrolytically active in the pH range 6-7, when tested with para-nitrophenyl-α-L-fucopyranoside (pNP-Fuc) as the substrate. In contrast, one fucosidase (Mfuc6) exhibited a high pH optimum and an unusual sigmoidal kinetics towards pNP-Fuc substrate. When tested for trans-fucosylation activity using pNP-Fuc as donor, most of the enzymes were able to transfer fucose to pNP-Fuc (self-condensation) or to lactose. With the α-L-fucosidase from Thermotoga maritima and the metagenome-derived Mfuc5, different fucosyllactose variants including the principal fucosylated HMO 2'-fucosyllactose were synthesised in yields of up to ~6.4%. Mfuc5 was able to release fucose from xyloglucan and could also use it as a fucosyl-donor for synthesis of fucosyllactose. This is the first study describing the use of glycosyl hydrolases for the synthesis of genuine fucosylated human milk oligosaccharides.

Alsayed Mostafa, Seongwon Im, Young‐Chae Song et al.

Processes • 2020

Since the observation of direct interspecies electron transfer (DIET) in anaerobic mixed cultures in 2010s, the topic “DIET-stimulation” has been the main route to enhance the performance of anaerobic digestion (AD) under harsh conditions, such as high organic loading rate (OLR) and the toxicants’ presence. In this review article, we tried to answer three main questions: (i) What are the merits and strategies for DIET stimulation? (ii) What are the consequences of stimulation? (iii) What is the mechanism of action behind the impact of this stimulation? Therefore, we introduced DIET history and recent relevant findings with a focus on the theoretical advantages. Then, we reviewed the most recent articles by categorizing how DIET reaction was stimulated by adding conductive material (CM) and/or applying external voltage (EV). The emphasis was made on the enhanced performance (yield and/or production rate), CM type, applied EV, and mechanism of action for each stimulation strategy. In addition, we explained DIET-caused changes in microbial community structure. Finally, future perspectives and practical limitations/chances were explored in detail. We expect this review article will provide a better understanding for DIET pathway in AD and encourage further research development in a right direction.

Avihai Zolti, Stefan J. Green, Noa Sela et al.

Microbiome • 2020

We demonstrate here that microbial profiling can elucidate stress signals that cannot be observed even through interrogation of host transcriptome, leading to an alternate mechanism for evaluating in situ conditions experienced by host organisms. This study is a proof-of-concept for the use of microbial communities as microsensors, with great potential for interrogation of a wide range of host systems. Video Abstract.

Jiawei Zhang, Hongpo Dong, Lijun Hou et al.

The ISME Journal • 2021

Asgard archaea are widely distributed in anaerobic environments. Previous studies revealed the potential capability of Asgard archaea to utilize various organic substrates including proteins, carbohydrates, fatty acids, amino acids and hydrocarbons, suggesting that Asgard archaea play an important role in sediment carbon cycling. Here, we describe a previously unrecognized archaeal phylum, Hermodarchaeota, affiliated with the Asgard superphylum. The genomes of these archaea were recovered from metagenomes generated from mangrove sediments, and were found to encode alkyl/benzyl-succinate synthases and their activating enzymes that are similar to those identified in alkane-degrading sulfate-reducing bacteria. Hermodarchaeota also encode enzymes potentially involved in alkyl-coenzyme A and benzoyl-coenzyme A oxidation, the Wood-Ljungdahl pathway and nitrate reduction. These results indicate that members of this phylum have the potential to strictly anaerobically degrade alkanes and aromatic compounds, coupling the reduction of nitrate. By screening Sequence Read Archive, additional genes encoding 16S rRNA and alkyl/benzyl-succinate synthases analogous to those in Hermodarchaeota were identified in metagenomic datasets from a wide range of marine and freshwater sediments. These findings suggest that Asgard archaea capable of degrading alkanes and aromatics via formation of alkyl/benzyl-substituted succinates are ubiquitous in sediments.

Muhammad Yousuf Jat Baloch, Wenjing Zhang, Tahira Sultana et al.

Environmental Technology & Innovation • 2023

Saline-alkali soil has become significant problem for global agriculture and food security as these soils have poor physicochemical conditions and reduce crop production by causing a wide range of physiological and biochemical changes in plants. More than 800 million hectares (Mha) of land throughout the world affected by saline-alkali soil, which accounts for 6% of the world total land area and about 62 Mha or 20% of the world’s irrigated land is affected by saline-alkali soil. Numerous studies on saline-alkali soils have been conducted throughout the years in an attempt to reduce plant productivity losses. Utilizing sewage sludge (SS) is an efficient way to improve saline-alkali soil and its physiochemical properties for plant productivity and improve soil’s health and crop yield. However, the in-depth mechanisms for the utilization of sewage sludge, their nutrient levels, toxic and harmful substances such as heavy metals, pathogenic microorganisms, antibiotics, and resistant genes that affect crop yield, groundwater quality, and ecological risks are still uncertain. This review enhances the awareness and knowledge to explore the sustainable mode of SS utilization in saline-alkali soil for the crop growth with crop rhizosphere effect, saline-alkali soil micro-ecology, carbon and nitrogen cycle enhancement. The potential future perspectives and research limitations for the utilization of SS for the crop production in saline-alkali soil are also discussed in review article.

Simone Zuffa, Patrick Schimmel, Ayoze Gonzalez-Santana et al.

Translational Psychiatry • 2023

Abstract Evidence from cross-sectional human studies, and preliminary microbial-based intervention studies, have implicated the microbiota-gut-brain axis in the neurobiology of autism spectrum disorder (ASD). Using a prospective longitudinal study design, we investigated the developmental profile of the fecal microbiota and metabolome in infants with ( n = 16) and without ( n = 19) a family history of ASD across the first 36 months of life. In addition, the general developmental levels of infants were evaluated using the Mullen Scales of Early Learning (MSEL) test at 5 and 36 months of age, and with ADOS-2 at 36 months of age. At 5 months of age, infants at elevated-likelihood of ASD (EL) harbored less Bifidobacterium and more Clostridium and Klebsiella species compared to the low-likelihood infants (LL). Untargeted metabolic profiling highlighted that LL infants excreted a greater amount of fecal γ-aminobutyric acid (GABA) at 5 months, which progressively declined with age. Similar age-dependent patterns were not observed in the EL group, with GABA being consistently low across all timepoints. Integrated microbiome-metabolome analysis showed a positive correlation between GABA and Bifidobacterium species and negative associations with Clostridium species. In vitro experiments supported these observations demonstrating that bifidobacteria can produce GABA while clostridia can consume it. At the behavioral level, there were no significant differences between the EL and LL groups at 5 months. However, at 36 months of age, the EL group had significantly lower MSEL and ADOS-2 scores compared to the LL group. Taken together, the present results reveal early life alterations in gut microbiota composition and functionality in infants at elevated-likelihood of ASD. These changes occur before any behavioral impairments can be detected, supporting a possible role for the gut microbiota in emerging behavioral variability later in life.

Mun Fai Loke, Eng Guan Chua, Han Ming Gan et al.

PLoS ONE • 2018

Colorectal cancer (CRC) is ranked the third most common cancer in human worldwide. However, the exact mechanisms of CRC are not well established. Furthermore, there may be differences between mechanisms of CRC in the Asian and in the Western populations. In the present study, we utilized a liquid chromatography-mass spectrometry (LC-MS) metabolomic approach supported by the 16S rRNA next-generation sequencing to investigate the functional and taxonomical differences between paired tumor and unaffected (normal) surgical biopsy tissues from 17 Malaysian patients. Metabolomic differences associated with steroid biosynthesis, terpenoid biosynthesis and bile metabolism could be attributed to microbiome differences between normal and tumor sites. The relative abundances of Anaerotruncus, Intestinimonas and Oscillibacter displayed significant relationships with both steroid biosynthesis and terpenoid and triterpenoid biosynthesis pathways. Metabolites involved in serotonergic synapse/ tryptophan metabolism (Serotonin and 5-Hydroxy-3-indoleacetic acid [5-HIAA]) were only detected in normal tissue samples. On the other hand, S-Adenosyl-L-homocysteine (SAH), a metabolite involves in methionine metabolism and methylation, was frequently increased in tumor relative to normal tissues. In conclusion, this study suggests that local microbiome dysbiosis may contribute to functional changes at the cancer sites. Results from the current study also contributed to the list of metabolites that are found to differ between normal and tumor sites in CRC and supported our quest for understanding the mechanisms of carcinogenesis.

Lauren E. Manck, Jiwoon Park, Benjamin Tully et al.

The ISME Journal • 2021

It is now widely accepted that siderophores play a role in marine iron biogeochemical cycling. However, the mechanisms by which siderophores affect the availability of iron from specific sources and the resulting significance of these processes on iron biogeochemical cycling as a whole have remained largely untested. In this study, we develop a model system for testing the effects of siderophore production on iron bioavailability using the marine copiotroph Alteromonas macleodii ATCC 27126. Through the generation of the knockout cell line ΔasbB::km r , which lacks siderophore biosynthetic capabilities, we demonstrate that the production of the siderophore petrobactin enables the acquisition of iron from mineral sources and weaker iron-ligand complexes. Notably, the utilization of lithogenic iron, such as that from atmospheric dust, indicates a significant role for siderophores in the incorporation of new iron into marine systems. We have also detected petrobactin, a photoreactive siderophore, directly from seawater in the mid-latitudes of the North Pacific and have identified the biosynthetic pathway for petrobactin in bacterial metagenome-assembled genomes widely distributed across the global ocean. Together, these results improve our mechanistic understanding of the role of siderophore production in iron biogeochemical cycling in the marine environment wherein iron speciation, bioavailability, and residence time can be directly influenced by microbial activities.

Krithika Arumugam, Irina Bessarab, Mindia Haryono et al.

npj Biofilms and Microbiomes • 2021

New long read sequencing technologies offer huge potential for effective recovery of complete, closed genomes from complex microbial communities. Using long read data (ONT MinION) obtained from an ensemble of activated sludge enrichment bioreactors we recover 22 closed or complete genomes of community members, including several species known to play key functional roles in wastewater bioprocesses, specifically microbes known to exhibit the polyphosphate- and glycogen-accumulating organism phenotypes (namely Candidatus Accumulibacter and Dechloromonas, and Micropruina, Defluviicoccus and Candidatus Contendobacter, respectively), and filamentous bacteria (Thiothrix) associated with the formation and stability of activated sludge flocs. Additionally we demonstrate the recovery of close to 100 circularised plasmids, phages and small microbial genomes from these microbial communities using long read assembled sequence. We describe methods for validating long read assembled genomes using their counterpart short read metagenome-assembled genomes, and assess the influence of different correction procedures on genome quality and predicted gene quality. Our findings establish the feasibility of performing long read metagenome-assembled genome recovery for both chromosomal and non-chromosomal replicons, and demonstrate the value of parallel sampling of moderately complex enrichment communities to obtaining high quality reference genomes of key functional species relevant for wastewater bioprocesses.

Zhongkai Zhou, Yuyang Wang, Yumei Jiang et al.

Lipids in Health and Disease • 2016

This study investigated the negative effect of DFEO on health, in which DFEO could impair glycerolipid metabolism, destroy gut histological structure and unbalance microbiota profile. More importantly, this is the first attempt to reveal the mechanism involved in these changes, which may provide the guideline for designing health diet.

Kazuki Nakamura, Ryo Iizuka, Shinro Nishi et al.

Scientific Reports • 2016

Environmental microbes are a great source of industrially valuable enzymes with potent and unique catalytic activities. Unfortunately, the majority of microbes remain unculturable and thus are not accessible by culture-based methods. Recently, culture-independent metagenomic approaches have been successfully applied, opening access to untapped genetic resources. Here we present a methodological approach for the identification of genes that encode metabolically active enzymes in environmental microbes in a culture-independent manner. Our method is based on activity-based single-cell sequencing, which focuses on microbial cells showing specific enzymatic activities. First, at the single-cell level, environmental microbes were encapsulated in water-in-oil microdroplets with a fluorogenic substrate for the target enzyme to screen for microdroplets that contain microbially active cells. Second, the microbial cells were recovered and subjected to whole genome amplification. Finally, the amplified genomes were sequenced to identify the genes encoding target enzymes. Employing this method, we successfully identified 14 novel β-glucosidase genes from uncultured bacterial cells in marine samples. Our method contributes to the screening and identification of genes encoding industrially valuable enzymes.

Ye Huang, Dake Xu, Luyao Huang et al.

npj Biofilms and Microbiomes • 2021

The process of microbiologically influenced corrosion (MIC) in soils has received widespread attention. Herein, long-term outdoor soil burial experiments were conducted to elucidate the community composition and functional interaction of soil microorganisms associated with metal corrosion. The results indicated that iron-oxidizing (e.g., Gallionella), nitrifying (e.g., Nitrospira), and denitrifying (e.g., Hydrogenophaga) microorganisms were significantly enriched in response to metal corrosion and were positively correlated with the metal mass loss. Corrosion process may promote the preferential growth of the abundant microbes. The functional annotation revealed that the metabolic processes of nitrogen cycling and electron transfer pathways were strengthened, and also that the corrosion of metals in soil was closely associated with the biogeochemical cycling of iron and nitrogen elements and extracellular electron transfer. Niche disturbance of microbial communities induced by the buried metals facilitated the synergetic effect of the major MIC participants. The co-occurrence network analysis suggested possible niche correlations among corrosion related bioindicators.

Minglei Ren, Jianjun Wang

The ISME Journal • 2022

Thaumarchaeota (now the class Nitrososphaeria in the phylum Thermoproteota in GTDB taxonomy) are abundant across marine and soil habitats; however, their genomic diversity and evolutionary history in freshwater environments remain elusive. Here, we reconstructed 17 high-quality metagenome-assembled genomes of Nitrososphaeria from a deep lake and two great rivers, and compared all available genomes between freshwater and marine habitats regarding their phylogenetic positions, relative abundance, and genomic content. We found that freshwater Nitrososphaeria were dominated by the family Nitrosopumilaceae and could be grouped into three distinct clades closely related to the genera Nitrosopumilus, Nitrosoarchaeum, and Nitrosotenuis. The Nitrosopumilus-like clade was exclusively from deep lakes, while the Nitrosoarchaeum-like clade was dominated by species from deep lakes and rivers, and the Nitrosotenuis-like clade was mainly from rivers, deep lakes, and estuaries. Interestingly, there was vertical niche separation between two clades in deep lakes, showing that the Nitrosopumilus-like species dominated shallow layers, whereas the relative abundance of the Nitrosoarchaeum-like clade increased toward deep waters. Phylogenetic clustering patterns in the Nitrosopumilaceae supported at least one freshwater-to-marine and two marine-to-freshwater transitions, the former of which refined the potential terrestrial-to-marine evolutionary path as previously proposed. The occurrence of the two marine-to-freshwater transitions were accompanied by horizontal transfer of the genes involved in nutrition regulation, osmoregulation, and cell motility during their colonization to freshwater habitats. Specifically, the Nitrosopumilus-like clade showed losses of genes encoding flagella assembly and ion transport, whereas the Nitrosoarchaeum-like clade had losses of intact genes involved in urea uptake and utilization and gains of genes encoding osmolarity-mediated mechanosensitive channels. Collectively, our results reveal for the first time the high genomic diversity of the class Nitrososphaeria across freshwater ecosystems and provide novel insights into their adaptive mechanisms and evolutionary histories.

Julie Cosmidis, Alexis S. Templeton

Nature Communications • 2016

In natural and laboratory-based environments experiencing sustained counter fluxes of sulfide and oxidants, elemental sulfur (S(0))-a key intermediate in the sulfur cycle-can commonly accumulate. S(0) is frequently invoked as a biomineralization product generated by enzymatic oxidation of hydrogen sulfide and polysulfides. Here we show the formation of S(0) encapsulated in nanometre to micrometre-scale tubular and spherical organic structures that self-assemble in sulfide gradient environments in the absence of any direct biological activity. The morphology and composition of these carbon/sulfur microstructures so closely resemble microbial cellular and extracellular structures that new caution must be applied to the interpretation of putative microbial biosignatures in the fossil record. These reactions between sulfide and organic matter have important implications for our understanding of S(0) mineralization processes and sulfur interactions with organic carbon in the environment. They furthermore provide a new pathway for the synthesis of carbon-sulfur nanocomposites for energy storage technologies.

Jonathan P. Badalamenti, Zarath M. Summers, Chi Ho Chan et al.

Frontiers in Microbiology • 2016

Reaching a depth of 713 m below the surface, the Soudan Underground Iron Mine (Soudan, MN, USA) transects a massive Archaean (2.7 Ga) banded iron formation, providing a remarkably accessible window into the terrestrial deep biosphere. Despite organic carbon limitation, metal-reducing microbial communities are present in potentially ancient anoxic brines continuously emanating from exploratory boreholes on Level 27. Using graphite electrodes deposited in situ as bait, we electrochemically enriched and isolated a novel halophilic iron-reducing Deltaproteobacterium, 'Desulfuromonas soudanensis' strain WTL, from an acetate-fed three-electrode bioreactor poised at +0.24 V (vs. standard hydrogen electrode). Cyclic voltammetry revealed that 'D. soudanensis' releases electrons at redox potentials approximately 100 mV more positive than the model freshwater surface isolate Geobacter sulfurreducens, suggesting that its extracellular respiration is tuned for higher potential electron acceptors. 'D. soudanensis' contains a 3,958,620-bp circular genome, assembled to completion using single-molecule real-time (SMRT) sequencing reads, which encodes a complete TCA cycle, 38 putative multiheme c-type cytochromes, one of which contains 69 heme-binding motifs, and a LuxI/LuxR quorum sensing cassette that produces an unidentified N-acyl homoserine lactone. Another cytochrome is predicted to lie within a putative prophage, suggesting that horizontal gene transfer plays a role in respiratory flexibility among metal reducers. Isolation of 'D. soudanensis' underscores the utility of electrode-based approaches for enriching rare metal reducers from a wide range of habitats.

Anna Edlund, Youngik Yang, Shibu Yooseph et al.

Microbiome • 2018

It is highly regarded that acidic conditions in dental plaque cause a net loss of enamel from teeth. Here, as pH drops below 5.5 pH to 4.7, we observe blooms of cariogenic lactobacilli, and a transition point of many bacterial gene expression activities within the community. To our knowledge, this represents the first study of the assembly and maturation of a complex oral bacterial biofilm community that addresses gene level functional responses over time.

Martin Smith, Marjorie Bardiau, Richard G. Brennan et al.

npj Materials Degradation • 2019

Abstract Accelerated low water corrosion is a form of marine steel corrosion caused by bacterial activity. It has a global spread and is potentially responsible for billions of pounds of damage. We have determined in detail both the chemistry of corrosion products and the associated microbiology at a UK site. The corrosion products form a layered structure with iron sulfides at the steel surface and iron oxides and sulfates in contact with water. The iron sulfides are formed by reaction of steel with hydrogen sulfide formed by sulfate-reducing bacteria and are oxidised through a series of sulfur oxidation states by sulfide-oxidising bacteria, forming acid at all stages and encompassing the whole of the bacterial sulfur cycle. The bacteria involved are endemic in anoxic bed sediment, and the process is a response to the presence of steel as an electron donor, and the generation of anoxic microenvironments within corrosion products.

Biao Li, Jiadong Sun, Chen Tang et al.

Water Research • 2020

Olga V. Karnachuk, I. I. Rusanov, И. А. Панова et al.

Scientific Reports • 2021

There is still a lack of understanding of H 2 S formation in agricultural waste, which leads to poor odour prevention and control. Microbial sulfate reduction is a major process contributing to sulfide formation in natural and technogenic environments with high sulfate and low oxygen concentration. Agricultural waste can be considered a low-sulfate system with no obvious input of oxidised sulfur compounds. The purpose of this study was to characterise a microbial community participating in H 2 S production and estimate the microbial sulfate reduction rate (SRR) in manure slurry from a large-scale swine finishing facility in Western Siberia. In a series of manure slurry microcosms, we identified bacterial consortia by 16S rRNA gene profiling and metagenomic analysis and revealed that sulfate-reducing Desulfovibrio were key players responsible for H 2 S production. The SRR measured with radioactive sulfate in manure slurry was high and comprised 7.25 nmol S cm -3 day -1 . Gypsum may be used as a solid-phase electron acceptor for sulfate reduction. Another plausible source of sulfate is a swine diet, which often contains supplements in the form of sulfates, including lysine sulfate. Low-sulfur diet, manure treatment with iron salts, and avoiding gypsum bedding are possible ways to mitigate H 2 S emissions from swine manure.

Yijing Chen, Yijing Chen, Yinhu Li et al.

Gut Microbes • 2024

The gut microbiota (GM) and its metabolites affect the host nervous system and are involved in the pathogeneses of various neurological diseases. However, the specific GM alterations under pathogenetic pressure and their contributions to the "microbiota - metabolite - brain axis" in Alzheimer's disease (AD) remain unclear. Here, we investigated the GM and the fecal, serum, cortical metabolomes in APP/PS1 and wild-type (WT) mice, revealing distinct hub bacteria in AD mice within scale-free GM networks shared by both groups. Moreover, we identified diverse peripheral - central metabolic landscapes between AD and WT mice that featured bile acids (e.g. deoxycholic and isodeoxycholic acid) and unsaturated fatty acids (e.g. 11Z-eicosenoic and palmitoleic acid). Machine-learning models revealed the relationships between the differential/hub bacteria and these metabolic signatures from the periphery to the brain. Notably, AD-enriched Dubosiella affected AD occurrence via cortical palmitoleic acid and vice versa. Considering the transgenic background of the AD mice, we propose that Dubosiella enrichment impedes AD progression via the synthesis of palmitoleic acid, which has protective properties against inflammation and metabolic disorders. We identified another association involving fecal deoxycholic acid-mediated interactions between the AD hub bacteria Erysipelatoclostridium and AD occurrence, which was corroborated by the correlation between deoxycholate levels and cognitive scores in humans. Overall, this study elucidated the GM network alterations, contributions of the GM to peripheral - central metabolic landscapes, and mediatory roles of metabolites between the GM and AD occurrence, thus revealing the critical roles of bacteria in AD pathogenesis and gut - brain communications under pathogenetic pressure.

Eric F. Lucking, Karen M. O’Connor, Conall Strain et al.

EBioMedicine • 2018

The Department of Physiology, and APC Microbiome Ireland, UCC.

Johannes Oppermann, P. Fischer, Arita Silapētere et al.

Nature Communications • 2019

Channelrhodopsins (ChRs) are algal light-gated ion channels widely used as optogenetic tools for manipulating neuronal activity. ChRs desensitize under continuous bright-light illumination, resulting in a significant decline of photocurrents. Here we describe a metagenomically identified family of phylogenetically distinct anion-conducting ChRs (designated MerMAIDs). MerMAIDs almost completely desensitize during continuous illumination due to accumulation of a late non-conducting photointermediate that disrupts the ion permeation pathway. MerMAID desensitization can be fully explained by a single photocycle in which a long-lived desensitized state follows the short-lived conducting state. A conserved cysteine is the critical factor in desensitization, as its mutation results in recovery of large stationary photocurrents. The rapid desensitization of MerMAIDs enables their use as optogenetic silencers for transient suppression of individual action potentials without affecting subsequent spiking during continuous illumination. Our results could facilitate the development of optogenetic tools from metagenomic databases and enhance general understanding of ChR function.