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Fiard M, Militon C, Sylvi L, Migeot J, Michaud E, Jézéquel R, Gilbert F, Bihannic I, Devesa J, Dirberg G, Cuny P. Uncovering potential mangrove microbial bioindicators to assess urban and agricultural pressures on Martinique island in the eastern Caribbean Sea. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 928:172217. [PMID: 38583633 DOI: 10.1016/j.scitotenv.2024.172217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 04/02/2024] [Accepted: 04/02/2024] [Indexed: 04/09/2024]
Abstract
Martinique's mangroves, which cover 1.85 ha of the island (<0.1 % of the total area), are considerably vulnerable to local urban, agricultural, and industrial pollutants. Unlike for temperate ecosystems, there are limited indicators that can be used to assess the anthropogenic pressures on mangroves. This study investigated four stations on Martinique Island, with each being subject to varying anthropogenic pressures. An analysis of mangrove sediment cores approximately 18 cm in depth revealed two primary types of pressures on Martinique mangroves: (i) an enrichment in organic matter in the two stations within the highly urbanized bay of Fort-de-France and (ii) agricultural pressure observed in the four studied mangrove stations. This pressure was characterized by contamination, exceeding the regulatory thresholds, with dieldrin, total DDT, and metals (As, Cu and Ni) found in phytosanitary products. The mangroves of Martinique are subjected to varying degrees of anthropogenic pressure, but all are subjected to contamination by organochlorine pesticides. Mangroves within the bay of Fort-de-France experience notably higher pressures compared to those in the island's northern and southern regions. In these contexts, the microbial communities exhibited distinct responses. The microbial biomass and the abundance of bacteria and archaea were higher in the two less-impacted stations, while in the mangrove of Fort-de-France, various phyla typically associated with polluted environments were more prevalent. These differences in the microbiota composition led to the identification of 65 taxa, including Acanthopleuribacteraceae, Spirochaetaceae, and Pirellulaceae, that could potentially serve as indicators of an anthropogenic influence on the mangrove sediments of Martinique Island.
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Affiliation(s)
- Maud Fiard
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
| | - Cécile Militon
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
| | - Léa Sylvi
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
| | - Jonathan Migeot
- Impact Mer consulting, expertise, and R&D firm, 20 rue Karukéra, 97200 Fort de France, Martinique/FWI, France.
| | - Emma Michaud
- Univ Brest, CNRS, IRD, Ifremer, LEMAR, 29280 Plouzané, France.
| | - Ronan Jézéquel
- CEDRE, 715 rue Alain Colas, 29218 Brest CEDEX 2, France.
| | - Franck Gilbert
- Laboratoire Écologie Fonctionnelle et Environnement, Université de Toulouse, CNRS, Toulouse INP, Université Toulouse 3 - Paul Sabatier, Toulouse, France.
| | | | - Jeremy Devesa
- Univ Brest, CNRS, IRD, Ifremer, LEMAR, 29280 Plouzané, France.
| | - Guillaume Dirberg
- Biologie des Organismes et Ecosystèmes Aquatiques (UMR 8067 BOREA) Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, IRD, UCN, UA, Rue Buffon, 75005 Paris, France.
| | - Philippe Cuny
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
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Li ZT, Song X, Yuan S, Zhao HP. Unveiling the inhibitory mechanisms of chromium exposure on microbial reductive dechlorination: Kinetics and microbial responses. WATER RESEARCH 2024; 253:121328. [PMID: 38382292 DOI: 10.1016/j.watres.2024.121328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 02/14/2024] [Accepted: 02/15/2024] [Indexed: 02/23/2024]
Abstract
Chromium and organochlorine solvents, particularly trichloroethene (TCE), are pervasive co-existing contaminants in subsurface aquifers due to their extensive industrial use and improper disposal practices. In this study, we investigated the microbial dechlorination kinetics under different TCE-Cr(Ⅲ/VI) composite pollution conditions and elucidated microbial response mechanisms based on community shift patterns and metagenomic analysis. Our results revealed that the reductive dechlorinating consortium had high resistance to Cr(III) but extreme sensitivity to Cr(VI) disturbance, resulting in a persistent inhibitory effect on subsequent dechlorination. Interestingly, the vinyl chloride-respiring organohalide-respiring bacteria (OHRB) was notably more susceptible to Cr(III/VI) exposure than the trichloroethene-respiring one, possibly due to inferior competition for growth substrates, such as electron donors. In terms of synergistic non-OHRB populations, Cr(III/VI) exposure had limited impacts on lactate fermentation but significantly interfered with H2-producing acetogenesis, leading to inhibited microbial dechlorination due to electron donor deficiencies. However, this inhibition can be effectively mitigated by the amendment of exogenous H2 supply. Furthermore, being the predominant OHRB, Dehalococcoides have inherent Cr(VI) resistance defects and collaborate with synergistic non-OHRB populations to achieve concurrent bio-detoxication of Cr(VI) and TCE. Our findings expand the understanding of the response patterns of different functional populations towards Cr(III/VI) stress, and provide valuable insights for the development of in situ bioremediation strategies for sites co-contaminated with chloroethene and chromium.
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Affiliation(s)
- Zheng-Tao Li
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310030, PR China
| | - Xin Song
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Songhu Yuan
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, No. 68 Jincheng Street, East Lake High-Tech Development Zone, Wuhan 430078, PR China
| | - He-Ping Zhao
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310030, PR China.
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Hessler T, Harrison ST, Banfield JF, Huddy RJ. Harnessing Fermentation May Enhance the Performance of Biological Sulfate-Reducing Bioreactors. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:2830-2846. [PMID: 38301118 PMCID: PMC10867827 DOI: 10.1021/acs.est.3c04187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 12/28/2023] [Accepted: 01/08/2024] [Indexed: 02/03/2024]
Abstract
Biological sulfate reduction (BSR) represents a promising strategy for bioremediation of sulfate-rich waste streams, yet the impact of metabolic interactions on performance is largely unexplored. Here, genome-resolved metagenomics was used to characterize 17 microbial communities in reactors treating synthetic sulfate-contaminated solutions. Reactors were supplemented with lactate or acetate and a small amount of fermentable substrate. Of the 163 genomes representing all the abundant bacteria, 130 encode 321 NiFe and FeFe hydrogenases and all genomes of the 22 sulfate-reducing microorganisms (SRM) encode genes for H2 uptake. We observed lactate oxidation solely in the first packed bed reactor zone, with propionate and acetate oxidation in the middle and predominantly acetate oxidation in the effluent zone. The energetics of these reactions are very different, yet sulfate reduction kinetics were unaffected by the type of electron donor available. We hypothesize that the comparable rates, despite the typically slow growth of SRM on acetate, are a result of the consumption of H2 generated by fermentation. This is supported by the sustained performance of a predominantly acetate-supplemented stirred tank reactor dominated by diverse fermentative bacteria encoding FeFe hydrogenase genes and SRM capable of acetate and hydrogen consumption and CO2 assimilation. Thus, addition of fermentable substrates to stimulate syntrophic relationships may improve the performance of BSR reactors supplemented with inexpensive acetate.
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Affiliation(s)
- Tomas Hessler
- The
Center for Bioprocess Engineering Research, University of Cape Town, Cape Town 7700, South Africa
- Department
of Chemical Engineering, University of Cape
Town, Cape Town 7700, South Africa
- The
Innovative Genomics Institute at the University of California, Berkeley, California CA94720, United
States
- The
Department of Earth and Planetary Science, University of California, Berkeley, California CA94720, United States
- Environmental
Genomics and Systems Biology Division, Lawrence
Berkeley National Laboratory, Berkeley, California CA94720, United States
| | - Susan T.L. Harrison
- The
Center for Bioprocess Engineering Research, University of Cape Town, Cape Town 7700, South Africa
- Department
of Chemical Engineering, University of Cape
Town, Cape Town 7700, South Africa
- The Future
Water Institute, University of Cape Town, Cape Town 7700, South Africa
| | - Jillian F. Banfield
- The
Innovative Genomics Institute at the University of California, Berkeley, California CA94720, United
States
- The
Department of Earth and Planetary Science, University of California, Berkeley, California CA94720, United States
- The
Department of Environmental Science, Policy and Management, University of California, Berkeley, California CA94720, United States
| | - Robert J. Huddy
- The
Center for Bioprocess Engineering Research, University of Cape Town, Cape Town 7700, South Africa
- Department
of Chemical Engineering, University of Cape
Town, Cape Town 7700, South Africa
- The Future
Water Institute, University of Cape Town, Cape Town 7700, South Africa
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Johnson LA, Dufour SC, Smith DDN, Manning AJ, Ahmed B, Binette S, Hamoutene D. Descriptive analyses of bacterial communities in marine sediment microcosms spiked with fish wastes, emamectin benzoate, and oxytetracycline. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 268:115683. [PMID: 37976931 DOI: 10.1016/j.ecoenv.2023.115683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 10/24/2023] [Accepted: 11/10/2023] [Indexed: 11/19/2023]
Abstract
In marine sediments surrounding salmon aquaculture sites, organic matter (OM) enrichment has been shown to influence resident bacterial community composition; however, additional effects on these communities due to combined use of the sea-lice therapeutant emamectin benzoate (EMB) and the widely used antibiotic oxytetracycline (OTC) are unknown. Here, we use sediment microcosms to assess the influence of OM, EMB, and OTC on benthic bacterial communities. Microcosms consisted of mud or sand sediments enriched with OM (fish and feed wastes) and spiked with EMB and OTC at environmentally-relevant concentrations. Samples were collected from initial matrices at the initiation of the trial and after 110 days for 16 S rRNA gene sequencing of the V3-V4 region and microbiome profiling. The addition of OM in both mud and sand sediments reduced alpha diversities; for example, an average of 1106 amplicon sequence variants (ASVs) were detected in mud with no OM addition, while only 729 and 596 ASVs were detected in mud with low OM and high OM, respectively. Sediments enriched with OM had higher relative abundances of Spirochaetota, Firmicutes, and Bacteroidota. For instance, Spirochaetota were detected in sediments with no OM with a relative abundance range of 0.01-1.2%, while in sediments enriched with OM relative abundance varied from 0.16% to 26.1%. In contrast, the addition of EMB (60 ng/g) or OTC (150 ng/g) did not result in distinct taxonomic shifts in the bacterial communities compared to un-spiked sediments during the timeline of this experiment. EMB and OTC concentrations may have been below effective inhibitor concentrations for taxa in these communities; further work should explore gene content and the presence of antibiotic resistance genes (ARGs) in sediment-dwelling bacteria.
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Affiliation(s)
- Lisa A Johnson
- St. Andrews Biological Station, Fisheries and Oceans Canada, St. Andrews, NB E5B 0E4, Canada
| | - Suzanne C Dufour
- Department of Biology, Memorial University of Newfoundland, St. John's, NL A1B 3X9, Canada
| | - Derek D N Smith
- Environment and Climate Change Canada, 335 River Road, Ottawa, ON K1V 1C7, Canada
| | - Anthony J Manning
- Research & Productivity Council (RPC), Fredericton, NB E3B 6Z9, Canada
| | - Bulbul Ahmed
- Research & Productivity Council (RPC), Fredericton, NB E3B 6Z9, Canada
| | - Sherry Binette
- Research & Productivity Council (RPC), Fredericton, NB E3B 6Z9, Canada
| | - Dounia Hamoutene
- St. Andrews Biological Station, Fisheries and Oceans Canada, St. Andrews, NB E5B 0E4, Canada.
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5
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Hirakata Y, Mei R, Morinaga K, Katayama T, Tamaki H, Meng XY, Watari T, Yamaguchi T, Hatamoto M, Nobu MK. Identification and cultivation of anaerobic bacterial scavengers of dead cells. THE ISME JOURNAL 2023; 17:2279-2289. [PMID: 37872273 PMCID: PMC10689501 DOI: 10.1038/s41396-023-01538-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 10/06/2023] [Accepted: 10/09/2023] [Indexed: 10/25/2023]
Abstract
The cycle of life and death and Earth's carbon cycle(s) are intimately linked, yet how bacterial cells, one of the largest pools of biomass on Earth, are recycled back into the carbon cycle remains enigmatic. In particular, no bacteria capable of scavenging dead cells in oxygen-depleted environments have been reported thus far. In this study, we discover the first anaerobes that scavenge dead cells and the two isolated strains use distinct strategies. Based on live-cell imaging, transmission electron microscopy, and hydrolytic enzyme assays, one strain (designated CYCD) relied on cell-to-cell contact and cell invagination for degrading dead food bacteria where as the other strain (MGCD) degraded dead food bacteria via excretion of lytic extracellular enzymes. Both strains could degrade dead cells of differing taxonomy (bacteria and archaea) and differing extents of cell damage, including those without artificially inflicted physical damage. In addition, both depended on symbiotic metabolic interactions for maximizing cell degradation, representing the first cultured syntrophic Bacteroidota. We collectively revealed multiple symbiotic bacterial decomposition routes of dead prokaryotic cells, providing novel insight into the last step of the carbon cycle.
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Affiliation(s)
- Yuga Hirakata
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8566, Japan.
| | - Ran Mei
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8566, Japan
| | - Kana Morinaga
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8566, Japan
| | - Taiki Katayama
- Geomicrobiology Research Group, Research Institute for Geo-Resources and Environment, Geological Survey of Japan (GSJ), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8567, Japan
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8566, Japan
| | - Xian-Ying Meng
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8566, Japan
| | - Takahiro Watari
- Department of Civil and Environmental Engineering, Nagaoka University of Technology, Nagaoka, 940-2188, Japan
| | - Takashi Yamaguchi
- Department of Civil and Environmental Engineering, Nagaoka University of Technology, Nagaoka, 940-2188, Japan
- Department of Science of Technology Innovation, Nagaoka University of Technology, Nagaoka, 940-2188, Japan
| | - Masashi Hatamoto
- Department of Civil and Environmental Engineering, Nagaoka University of Technology, Nagaoka, 940-2188, Japan
| | - Masaru K Nobu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8566, Japan.
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, 237-0061, Japan.
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6
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Nguyen TQ, Martínez-Álvaro M, Lima J, Auffret MD, Rutherford KMD, Simm G, Dewhurst RJ, Baima ET, Roehe R. Identification of intestinal and fecal microbial biomarkers using a porcine social stress model. Front Microbiol 2023; 14:1197371. [PMID: 38029169 PMCID: PMC10670831 DOI: 10.3389/fmicb.2023.1197371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 10/20/2023] [Indexed: 12/01/2023] Open
Abstract
Understanding the relationships between social stress and the gastrointestinal microbiota, and how they influence host health and performance is expected to have many scientific and commercial implementations in different species, including identification and improvement of challenges to animal welfare and health. In particular, the study of the stress impact on the gastrointestinal microbiota of pigs may be of interest as a model for human health. A porcine stress model based on repeated regrouping and reduced space allowance during the last 4 weeks of the finishing period was developed to identify stress-induced changes in the gut microbiome composition. The application of the porcine stress model resulted in a significant increase in salivary cortisol concentration over the course of the trial and decreased growth performance and appetite. The applied social stress resulted in 32 bacteria being either enriched (13) or depleted (19) in the intestine and feces. Fecal samples showed a greater number of microbial genera influenced by stress than caecum or colon samples. Our trial revealed that the opportunistic pathogens Treponema and Clostridium were enriched in colonic and fecal samples from stressed pigs. Additionally, genera such as Streptococcus, Parabacteroides, Desulfovibrio, Terrisporobacter, Marvinbryantia, and Romboutsia were found to be enriched in response to social stress. In contrast, the genera Prevotella, Faecalibacterium, Butyricicoccus, Dialister, Alloprevotella, Megasphaera, and Mitsuokella were depleted. These depleted bacteria are of great interest because they synthesize metabolites [e.g., short-chain fatty acids (SCFA), in particular, butyrate] showing beneficial health benefits due to inhibitory effects on pathogenic bacteria in different animal species. Of particular interest are Dialister and Faecalibacterium, as their depletion was identified in a human study to be associated with inferior quality of life and depression. We also revealed that some pigs were more susceptible to pathogens as indicated by large enrichments of opportunistic pathogens of Clostridium, Treponema, Streptococcus and Campylobacter. Generally, our results provide further evidence for the microbiota-gut-brain axis as indicated by an increase in cortisol concentration due to social stress regulated by the hypothalamic-pituitary-adrenal axis, and a change in microbiota composition, particularly of bacteria known to be associated with pathogenicity and mental health diseases.
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Affiliation(s)
- Tuan Q. Nguyen
- Scotland’s Rural College, Edinburgh, United Kingdom
- Department of Animal Breeding, Faculty of Animal Science and Veterinary Medicine, Nong Lam University – Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | | | - Joana Lima
- Scotland’s Rural College, Edinburgh, United Kingdom
| | | | | | - Geoff Simm
- Global Academy of Agriculture and Food Security, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Eric T. Baima
- Zoetis Inc., Parsippany-Troy Hills, NJ, United States
| | - Rainer Roehe
- Scotland’s Rural College, Edinburgh, United Kingdom
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Rellegadla S, Prajapat G, Jain S, Agrawal A. Microbial communities succession post to polymer flood demonstrate a role in enhanced oil recovery. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12673-3. [PMID: 37428189 DOI: 10.1007/s00253-023-12673-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 04/03/2023] [Accepted: 06/15/2023] [Indexed: 07/11/2023]
Abstract
The role of indigenous microbial communities in residual oil extraction following a recovery process is not well understood. This study investigated the dynamics of resident microbial communities in oil-field simulating sand pack bioreactors after the polymer flooding stage resumed with waterflooding and explored their contribution to the oil extraction process. The microbial community succession was studied through high-throughput sequencing of 16S rRNA genes. The results revealed alternating dominance of minority populations, including Dietzia sps., Acinetobacter sps., Soehngenia sps., and Paracoccus sps., in each bioreactor following the flooding process. Additionally, the post-polymer waterflooding stage led to higher oil recovery, with hydroxyethylcellulose, tragacanth gum, and partially hydrolyzed polyacrylamide polymer-treated bioreactors yielding additional recovery of 4.36%, 5.39%, and 3.90% residual oil in place, respectively. The dominant microbial communities were previously reported to synthesize biosurfactants and emulsifiers, as well as degrade and utilize hydrocarbons, indicating their role in aiding the recovery process. However, the correlation analysis of the most abundant taxa showed that some species were more positively correlated with the oil recovery process, while others acted as competitors for the carbon source. The study also found that higher biomass favored the plugging of high permeability zones in the reservoir, facilitating the dislodging of crude oil in new channels. In conclusion, this study suggests that microbial populations significantly shift upon polymer treatment and contribute synergistically to the oil recovery process depending on the characteristics of the polymers injected. KEY POINTS: • Post-polymer flooded microbial ecology shows unique indigenous microbial consortia. • Injected polymers are observed to act as enrichment substrates by resident communities. • The first study to show successive oil recovery stage post-polymer flood without external influence.
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Affiliation(s)
- Sandeep Rellegadla
- Energy and Environment Research Laboratory, Department of Microbiology, Central University of Rajasthan, NH-8, Bandersindri, Kishangarh, Ajmer, Rajasthan, 305817, India
- Centre for Water Technology, Department of Biological and Chemical Engineering, Aarhus University, Universitetsbyen 36, 8000, Aarhus C, Denmark
| | - Ganshyam Prajapat
- The Energy and Resources Institute (TERI), Darbari Seth Block, India Habitat Centre, Lodhi Road, New Delhi, 110003, India
| | - Shikha Jain
- Enercosm Pvt. Ltd., Jaipur, Rajasthan, 302019, India
| | - Akhil Agrawal
- Energy and Environment Research Laboratory, Department of Microbiology, Central University of Rajasthan, NH-8, Bandersindri, Kishangarh, Ajmer, Rajasthan, 305817, India.
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Frias H, Murga Valderrama NL, Flores GJ, Cornejo VG, Del Solar JC, Romani AC, Bardales W, Segura GT, Polveiro RC, Vieira DDS, Lopez Lapa RM, Maicelo Quintana JL. An analysis of the cecum microbiome of three breeds of the guinea pig: Andina, Inti, and Peru. Res Vet Sci 2023; 161:50-61. [PMID: 37321011 DOI: 10.1016/j.rvsc.2023.06.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/24/2023] [Accepted: 06/06/2023] [Indexed: 06/17/2023]
Abstract
This study investigated the effect of host genetics on the structure and composition of the cecum microbiota of three breeds of guinea pigs: Andina, Inti, and Peru. Fifteen guinea pigs were distributed into three groups according to their breed: Andina (5), Inti (5), and Peru (5). We discovered that four main phyla were shared between the three breeds: Bacteroidota, Firmicutes, Spirochaetota, and Synergistota. Although there were no significant differences in the alpha and beta diversity analysis, we found that the Linear discriminant analysis effect size and the heat tree analysis showed significant differences between the abundance of several taxa present in the cecum microbiome of the three breeds. These results suggest that host genetics could be a factor in the structure and composition of the guinea pig cecum microbiome. In addition, we found unique genera for each breed that have fermentation capacity and, therefore can be analyzed in further studies to determine if there is a functional relationship between them and the breed and its industrial profile.
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Affiliation(s)
- Hugo Frias
- Academic Department of Zootechnics, Faculty of Zootechnical Engineering, Agribusiness and Biotechnology, National University Toribio Rodríguez de Mendoza, Amazonas, Peru
| | - Nilton Luis Murga Valderrama
- Livestock and Biotechnology Research Institute, National University Toribio Rodríguez de Mendoza, Amazonas, Peru
| | - Gary J Flores
- Livestock and Biotechnology Research Institute, National University Toribio Rodríguez de Mendoza, Amazonas, Peru
| | - Victor G Cornejo
- Livestock and Biotechnology Research Institute, National University Toribio Rodríguez de Mendoza, Amazonas, Peru
| | - Jakson Ch Del Solar
- Livestock and Biotechnology Research Institute, National University Toribio Rodríguez de Mendoza, Amazonas, Peru
| | - Ana C Romani
- Livestock and Biotechnology Research Institute, National University Toribio Rodríguez de Mendoza, Amazonas, Peru
| | - William Bardales
- Laboratory of Infectious and Parasitic Diseases, Livestock and Biotechnology Research Institute, Faculty of Zootechnical Engineering, Agribusiness, and Biotechnology, National University Toribio Rodríguez de Mendoza, Amazonas, Peru
| | - G T Segura
- Livestock and Biotechnology Research Institute, National University Toribio Rodríguez de Mendoza, Amazonas, Peru
| | - Richard C Polveiro
- Laboratory of Bacterial Diseases, Sector of Preventive Veterinary Medicine and Public Health, Department of Veterinary, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Dielson da S Vieira
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Rainer M Lopez Lapa
- Livestock and Biotechnology Research Institute, National University Toribio Rodríguez de Mendoza, Amazonas, Peru; Department of Public Health, Faculty of Health Sciences, National University Toribio Rodríguez de Mendoza de Amazonas, Chachapoyas, Peru.
| | - Jorge Luis Maicelo Quintana
- Livestock and Biotechnology Research Institute, National University Toribio Rodríguez de Mendoza, Amazonas, Peru
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Wu Z, Yu X, Liu G, Li W, Lu L, Li P, Xu X, Jiang J, Wang B, Qiao W. Sustained detoxification of 1,2-dichloroethane to ethylene by a symbiotic consortium containing Dehalococcoides species. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 325:121443. [PMID: 36921661 DOI: 10.1016/j.envpol.2023.121443] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 02/19/2023] [Accepted: 03/11/2023] [Indexed: 06/18/2023]
Abstract
1,2-Dichloroethane (1,2-DCA) is a ubiquitous volatile halogenated organic pollutant in groundwater and soil, which poses a serious threat to the ecosystem and human health. Microbial reductive dechlorination has been recognized as an environmentally-friendly strategy for the remediation of sites contaminated with 1,2-DCA. In this study, we obtained an anaerobic microbiota derived from 1,2-DCA contaminated groundwater, which was able to sustainably convert 1,2-DCA into non-toxic ethylene with an average dechlorination rate of 30.70 ± 11.06 μM d-1 (N = 6). The microbial community profile demonstrated that the relative abundance of Dehalococcoides species increased from 0.53 ± 0.08% to 44.68 ± 3.61% in parallel with the dechlorination of 1,2-DCA. Quantitative PCR results showed that the Dehalococcoides species 16S rRNA gene increased from 2.40 ± 1.71 × 108 copies∙mL-1 culture to 4.07 ± 2.45 × 108 copies∙mL-1 culture after dechlorinating 110.69 ± 30.61 μmol of 1,2-DCA with a growth yield of 1.55 ± 0.93 × 108 cells per μmol Cl- released (N = 6), suggesting that Dehalococcoides species used 1,2-DCA for organohalide respiration to maintain cell growth. Notably, the relative abundances of Methanobacterium sp. (p = 0.0618) and Desulfovibrio sp. (p = 0.0001995) also increased significantly during the dechlorination of 1,2-DCA and were clustered in the same module with Dehalococcoides species in the co-occurrence network. These results hinted that Dehalococcoides species, the obligate organohalide-respiring bacterium, exhibited potential symbiotic relationships with Methanobacterium and Desulfovibrio species. This study illustrates the importance of microbial interactions within functional microbiota and provides a promising microbial resource for in situ bioremediation in sites contaminated with 1,2-DCA.
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Affiliation(s)
- Zhiming Wu
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xin Yu
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Guiping Liu
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Wei Li
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Lianghua Lu
- Jiangsu Provincial Key Laboratory of Environmental Engineering, Jiangsu Provincial Academy of Environmental Science, Nanjing 210036, China
| | - Pengfa Li
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xihui Xu
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiandong Jiang
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Baozhan Wang
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Wenjing Qiao
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China.
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10
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Deng Z, Zhang N, Jiang L, Liu H, Hu S, Zhang D, Chen B, Liu Q, Sun Y, Chen J, Zhang C. Influence of microplastics on microbial anaerobic detoxification of chlorophenols. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 316:120707. [PMID: 36427829 DOI: 10.1016/j.envpol.2022.120707] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 11/10/2022] [Accepted: 11/18/2022] [Indexed: 06/16/2023]
Abstract
Microplastics (MPs) can absorb halogenated organic compounds and transport them into marine anaerobic zones. Microbial reductive dehalogenation is a major process that naturally attenuates organohalide pollutants in anaerobic environments. Here, we aimed to determine the mechanisms through which MPs affect the microbe-mediated marine halogen cycle by incubating 2,4,6-trichlorophenol (TCP) dechlorinating cultures with various types of MPs. We found that TCP was dechlorinated to 4-chlorophenol in biotic control and polypropylene (PP) cultures, but essentially terminated at 2,4-dichlorophenol in polyethylene (PE) and polyethylene terephthalate (PET) cultures after incubation for 20 days. Oxygen-containing functional groups such as peroxide and aldehyde were enriched on PE and PET after incubation and corresponded to elevated levels of intracellular reactive oxygen species (ROS) in the microorganisms. Adding PE or PET to the cultures exerted limited effects on hydrogenase and ATPase activities, but delayed the expression of the gene encoding reductive dehalogenase (RDase). Considering the limited changes in the microbial composition of the enriched cultures, these findings suggested that microbial dechlorination is probably affected by MPs through the ROS-induced inhibition of RDase synthesis and/or activity. Overall, our findings showed that extensive MP pollution is unfavorable to environmental xenobiotic detoxification.
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Affiliation(s)
- Zhaochao Deng
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan, 316021, Zhejiang, China
| | - Ning Zhang
- Department of Environmental Engineering, School of Chemical Engineering and Pharmacy, Henan University of Science and Technology, Luoyang, 471000, Henan, China
| | - Lijia Jiang
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan, 316021, Zhejiang, China
| | - Hui Liu
- Shengzhou Bureau of Agriculture and Rural Affairs, Shaoxing, 312400, Zhejiang, China
| | - Songtao Hu
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan, 316021, Zhejiang, China
| | - Dongdong Zhang
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan, 316021, Zhejiang, China
| | - Bairu Chen
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan, 316021, Zhejiang, China
| | - Qing Liu
- The Guangxi Key Laboratory of Theory and Technology for Environmental Pollution Control, Guilin University of Technology, Guilin, 541006, Guangxi, China
| | - Yuxia Sun
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan, 316021, Zhejiang, China
| | - Jiawang Chen
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan, 316021, Zhejiang, China
| | - Chunfang Zhang
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan, 316021, Zhejiang, China.
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11
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Holland SI, Vázquez-Campos X, Ertan H, Edwards RJ, Manefield MJ, Lee M. Metaproteomics reveals methyltransferases implicated in dichloromethane and glycine betaine fermentation by ' Candidatus Formimonas warabiya' strain DCMF. Front Microbiol 2022; 13:1035247. [PMID: 36569084 PMCID: PMC9768040 DOI: 10.3389/fmicb.2022.1035247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 11/15/2022] [Indexed: 12/12/2022] Open
Abstract
Dichloromethane (DCM; CH2Cl2) is a widespread pollutant with anthropogenic and natural sources. Anaerobic DCM-dechlorinating bacteria use the Wood-Ljungdahl pathway, yet dechlorination reaction mechanisms remain unclear and the enzyme(s) responsible for carbon-chlorine bond cleavage have not been definitively identified. Of the three bacterial taxa known to carry out anaerobic dechlorination of DCM, 'Candidatus Formimonas warabiya' strain DCMF is the only organism that can also ferment non-chlorinated substrates, including quaternary amines (i.e., choline and glycine betaine) and methanol. Strain DCMF is present within enrichment culture DFE, which was derived from an organochlorine-contaminated aquifer. We utilized the metabolic versatility of strain DCMF to carry out comparative metaproteomics of cultures grown with DCM or glycine betaine. This revealed differential abundance of numerous proteins, including a methyltransferase gene cluster (the mec cassette) that was significantly more abundant during DCM degradation, as well as highly conserved amongst anaerobic DCM-degrading bacteria. This lends strong support to its involvement in DCM dechlorination. A putative glycine betaine methyltransferase was also discovered, adding to the limited knowledge about the fate of this widespread osmolyte in anoxic subsurface environments. Furthermore, the metagenome of enrichment culture DFE was assembled, resulting in five high quality and two low quality draft metagenome-assembled genomes. Metaproteogenomic analysis did not reveal any genes or proteins for utilization of DCM or glycine betaine in the cohabiting bacteria, supporting the previously held idea that they persist via necromass utilization.
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Affiliation(s)
- Sophie I. Holland
- Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, NSW, Australia
| | - Xabier Vázquez-Campos
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Haluk Ertan
- School of Chemical Engineering, University of New South Wales, Sydney, NSW, Australia,Department of Molecular Biology and Genetics, Istanbul University, Istanbul, Turkey
| | - Richard J. Edwards
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Michael J. Manefield
- Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, NSW, Australia,School of Chemical Engineering, University of New South Wales, Sydney, NSW, Australia
| | - Matthew Lee
- Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, NSW, Australia,*Correspondence: Matthew Lee,
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12
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Li J, Yao C, Song B, Zhang Z, Brock AL, Trapp S, Zhang J. Enrichment of sulfur-oxidizing bacteria using S-doped NiFe 2O 4 nanosheets as the anode in microbial fuel cell enhances power production and sulfur recovery. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 844:156973. [PMID: 35772559 DOI: 10.1016/j.scitotenv.2022.156973] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 06/05/2022] [Accepted: 06/21/2022] [Indexed: 06/15/2023]
Abstract
Microbial fuel cells (MFCs) have great promise for power generation by oxidizing organic wastewater, yet the challenge to realize high efficiency in simultaneous energy production and resource recovery remains. In this study, we designed a novel MFC anode by synthesizing S-doped NiFe2O4 nanosheet arrays on carbon cloth (S10-NiFe2O4@CC) to build a three-dimensional (3D) hierarchically porous structure, with the aim to regulate the microbial community of sulfur-cycling microbes in order to enhance power production and elemental sulfur (S0) recovery. The S10-NiFe2O4@CC anode obtained a faster start-up time of 2 d and the highest power density of 4.5 W/m2 in acetate-fed and mixed bacteria-based MFCs. More importantly, sulfide removal efficiency (98.3 %) (initial concentration of 50 mg/L S2-) could be achieved within 3 d and sulfur (S8) could be produced. Microbial community analysis revealed that the S10-NiFe2O4@CC anode markedly enriched sulfur-oxidizing bacteria (SOB) and promoted enrichment of SOB and sulfate-reducing bacteria (SRB) in the bulk solution as well, leading to the enhancement of power generation and S0 recovery. This study shows how carefully designing and optimizing the composition and structure of the anode can lead to the enrichment of a multifunctional microbiota with excellent potential for sulfide removal and resource recovery.
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Affiliation(s)
- Jiaxin Li
- National Engineering Laboratory for VOCs Pollution Control Material & Technology, Research Center for Environmental Material and Pollution Control Technology, University of Chinese Academy of Sciences, Beijing 101408, China; Department of Environmental Engineering, Technical University of Denmark, Bygningstorvet 115, 2800 Kongens Lyngby, Denmark; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Environmental Nanotechnology and Health Effects, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Chongchao Yao
- National Engineering Laboratory for VOCs Pollution Control Material & Technology, Research Center for Environmental Material and Pollution Control Technology, University of Chinese Academy of Sciences, Beijing 101408, China
| | - Bo Song
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Zhihao Zhang
- Key Laboratory of Environmental Nanotechnology and Health Effects, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Andreas Libonati Brock
- Department of Environmental Engineering, Technical University of Denmark, Bygningstorvet 115, 2800 Kongens Lyngby, Denmark
| | - Stefan Trapp
- Department of Environmental Engineering, Technical University of Denmark, Bygningstorvet 115, 2800 Kongens Lyngby, Denmark
| | - Jing Zhang
- National Engineering Laboratory for VOCs Pollution Control Material & Technology, Research Center for Environmental Material and Pollution Control Technology, University of Chinese Academy of Sciences, Beijing 101408, China; Key Laboratory of Environmental Nanotechnology and Health Effects, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
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13
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Guo S, Toth CRA, Luo F, Chen X, Xiao J, Edwards EA. Transient Oxygen Exposure Causes Profound and Lasting Changes to a Benzene-Degrading Methanogenic Community. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:13036-13045. [PMID: 36083837 PMCID: PMC9496526 DOI: 10.1021/acs.est.2c02624] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 08/22/2022] [Accepted: 08/26/2022] [Indexed: 06/15/2023]
Abstract
We investigated the impact of oxygen on a strictly anaerobic, methanogenic benzene-degrading enrichment culture derived decades ago from oil-contaminated sediment. The culture includes a benzene fermenter from Deltaproteobacteria candidate clade Sva0485 (referred to as ORM2) and methanogenic archaea. A one-time injection of 0.1 mL air , simulating a small leak into 30 mL batch culture bottle, had no measurable impact on benzene degradation rates, although retrospectively, a tiny enrichment of aerobic taxa was detected. A subsequent 100 times larger injection of air stalled methanogenesis and caused drastic perturbation of the microbial community. A benzene-degrading Pseudomonas became highly enriched and consumed all available oxygen. Anaerobic benzene-degrading ORM2 cell numbers plummeted during this time; re-growth and associated recovery of methanogenic benzene degradation took almost 1 year. These results highlight the oxygen sensitivity of this methanogenic culture and confirm that the mechanism for anaerobic biotransformation of benzene is independent of oxygen, fundamentally different from established aerobic pathways, and is carried out by distinct microbial communities. The study also highlights the importance of including microbial decay in characterizing and modeling mixed microbial communities.
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Affiliation(s)
| | | | | | - Xu Chen
- Department of Chemical Engineering
and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - Johnny Xiao
- Department of Chemical Engineering
and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - Elizabeth A. Edwards
- Department of Chemical Engineering
and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
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14
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Yu F, Luo W, Xie W, Li Y, Meng S, Kan J, Ye X, Peng T, Wang H, Huang T, Hu Z. Community reassemblies of eukaryotes, prokaryotes, and viruses in the hexabromocyclododecanes-contaminated microcosms. JOURNAL OF HAZARDOUS MATERIALS 2022; 436:129159. [PMID: 35643009 DOI: 10.1016/j.jhazmat.2022.129159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/28/2022] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
The microbial community in seriously contaminated environment were not well known. This research investigated the community reassemblies in microcosms made of two distinct mangrove sediments amended with high levels of hexabromocyclododecanes (HBCDs). After eight months of contamination, the transformation of HBCDs yielded various lower brominated products and resulted in acidification (pH ~2). Therefore, the degraders and dehalogenase homologous genes involved in transformation of HBCDs only presented in low abundance to avoid further deterioration of the habitats. Moreover, in these deteriorated habitats, 1344 bacterial, 969 archaeal, 599 eukaryotic (excluded fungi), 187 fungal OTUs, and 10 viral genera, were reduced compared with controls. Specifically, in two groups of microcosms, Zetaproteobacteria, Deinococcus-Thermus, Spirochaetes, Bacteroidetes, Euryarchaeota, and Ascomycota, were positively responding taxa to HBCDs. Caloneis (Bacillariophyta) and Ascomycota turned to the dominant eukaryotic and fungal taxa. Most of predominant taxa were related to the contamination of brominated flame retardants (BFRs). Microbial communities were reassembled in divergent and sediment-dependent manner. The long-term contamination of HBCDs leaded to the change of relations between many taxa, included some of the environmental viruses and their known hosts. This research highlight the importance of monitoring the ecological effects around plants producing or processing halogenated compounds.
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Affiliation(s)
- Fei Yu
- Department of Biology, College of Science, Shantou University, Guangdong Province, PR China
| | - Wenqi Luo
- Department of Biology, College of Science, Shantou University, Guangdong Province, PR China
| | - Wei Xie
- Department of Biology, College of Science, Shantou University, Guangdong Province, PR China
| | - Yuyang Li
- Department of Biology, College of Science, Shantou University, Guangdong Province, PR China
| | - Shanshan Meng
- Department of Biology, College of Science, Shantou University, Guangdong Province, PR China
| | - Jie Kan
- Department of Biology, College of Science, Shantou University, Guangdong Province, PR China
| | - Xueying Ye
- Department of Biology, College of Science, Shantou University, Guangdong Province, PR China
| | - Tao Peng
- Department of Biology, College of Science, Shantou University, Guangdong Province, PR China
| | - Hui Wang
- Department of Biology, College of Science, Shantou University, Guangdong Province, PR China
| | - Tongwang Huang
- Department of Biology, College of Science, Shantou University, Guangdong Province, PR China
| | - Zhong Hu
- Department of Biology, College of Science, Shantou University, Guangdong Province, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong, PR China.
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15
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Comparative Analysis of Brucepastera parasyntrophica gen. nov., sp. nov. and Teretinema zuelzerae gen. nov., comb. nov. ( Treponemataceae) Reveals the Importance of Interspecies Hydrogen Transfer in the Energy Metabolism of Spirochetes. Appl Environ Microbiol 2022; 88:e0050322. [PMID: 35862663 PMCID: PMC9317865 DOI: 10.1128/aem.00503-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Most members of the family Treponemataceae (Spirochaetales) are associated with vertebrate hosts. However, a diverse clade of uncultured, putatively free-living treponemes comprising several genus-level lineages is present in other anoxic environments. The only cultivated representative to date is Treponema zuelzerae, isolated from freshwater mud. Here, we describe the isolation of strain RmG11 from the intestinal tract of cockroaches. The strain represents a novel genus-level lineage of Treponemataceae and is metabolically distinct from T. zuelzerae. While T. zuelzerae grows well on various sugars, forming acetate and H2 as major fermentation products, strain RmG11 grew poorly on glucose, maltose, and starch, forming mainly ethanol and only small amounts of acetate and H2. In contrast to the growth of T. zuelzerae, that of strain RmG11 was strongly inhibited at high H2 partial pressures but improved considerably when H2 was removed from the headspace. Cocultures of strain RmG11 with the H2-consuming Methanospirillum hungatei produced acetate and methane but no ethanol. Comparative genomic analysis revealed that strain RmG11 possesses only a single, electron-confurcating hydrogenase that forms H2 from NADH and reduced ferredoxin, whereas T. zuelzerae also possesses a second, ferredoxin-dependent hydrogenase that allows the thermodynamically more favorable formation of H2 from ferredoxin via the Rnf complex. In addition, we found that T. zuelzerae utilizes xylan and possesses the genomic potential to degrade other plant polysaccharides. Based on phenotypic and phylogenomic evidence, we describe strain RmG11 as Brucepastera parasyntrophica gen. nov., sp. nov. and Treponema zuelzerae as Teretinema zuelzerae gen. nov., comb. nov. IMPORTANCE Spirochetes are widely distributed in various anoxic environments and commonly form molecular hydrogen as a major fermentation product. Here, we show that two closely related members of the family Treponemataceae differ strongly in their sensitivity to high hydrogen partial pressure, and we explain the metabolic mechanisms that cause these differences by comparative genome analysis. We demonstrate a strong boost in the growth of the hydrogen-sensitive strain and a shift in its fermentation products to acetate during cocultivation with a H2-utilizing methanogen. Our results add a hitherto unrecognized facet to the fermentative metabolism of spirochetes and also underscore the importance of interspecies hydrogen transfer in not-obligately-syntrophic interactions among fermentative and hydrogenotrophic guilds in anoxic environments.
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16
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Zhu QZ, Wegener G, Hinrichs KU, Elvert M. Activity of Ancillary Heterotrophic Community Members in Anaerobic Methane-Oxidizing Cultures. Front Microbiol 2022; 13:912299. [PMID: 35722308 PMCID: PMC9201399 DOI: 10.3389/fmicb.2022.912299] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 05/02/2022] [Indexed: 11/13/2022] Open
Abstract
Consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria mediate the anaerobic oxidation of methane (AOM) in marine sediments. However, even sediment-free cultures contain a substantial number of additional microorganisms not directly related to AOM. To track the heterotrophic activity of these community members and their possible relationship with AOM, we amended meso- (37°C) and thermophilic (50°C) AOM cultures (dominated by ANME-1 archaea and their partner bacteria of the Seep-SRB2 clade or Candidatus Desulfofervidus auxilii) with L-leucine-3-13C (13C-leu). Various microbial lipids incorporated the labeled carbon from this amino acid, independent of the presence of methane as an energy source, specifically bacterial fatty acids, such as iso and anteiso-branched C15:0 and C17:0, as well as unsaturated C18:1ω9 and C18:1ω7. In natural methane-rich environments, these bacterial fatty acids are strongly 13C-depleted. We, therefore, suggest that those fatty acids are produced by ancillary bacteria that grow on 13C-depleted necromass or cell exudates/lysates of the AOM core communities. Candidates that likely benefit from AOM biomass are heterotrophic bacterial members of the Spirochetes and Anaerolineae—known to produce abundant branched fatty acids and present in all the AOM enrichment cultures. For archaeal lipids, we observed minor 13C-incorporation, but still suggesting some 13C-leu anabolism. Based on their relatively high abundance in the culture, the most probable archaeal candidates are Bathyarchaeota, Thermoplasmatales, and Lokiarchaeota. The identified heterotrophic bacterial and archaeal ancillary members are likely key players in organic carbon recycling in anoxic marine sediments.
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Affiliation(s)
- Qing-Zeng Zhu
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Gunter Wegener
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.,Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Kai-Uwe Hinrichs
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.,Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Marcus Elvert
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.,Faculty of Geosciences, University of Bremen, Bremen, Germany
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17
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Quorum quenching of autoinducer 2 increases methane production in anaerobic digestion of waste activated sludge. Appl Microbiol Biotechnol 2022; 106:4763-4774. [PMID: 35715650 DOI: 10.1007/s00253-022-12014-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/02/2022] [Accepted: 06/04/2022] [Indexed: 11/02/2022]
Abstract
The ubiquitous signaling molecule autoinducer 2 (AI-2) is involved in intra- and interspecies communication, most notably between Gram-negative and Gram-positive bacteria. AI-2 accumulates during the exponential phase of the Escherichia coli (E. coli) monoculture and then rapidly decreases upon entry into the stationary phase. However, deleting both the genes encoding AI-2 synthase (LuxS) and the lsr operon regulator (LsrR) in the E. coli genome causes impaired AI-2 production and continuous AI-2 scavenging from the environment. This genetically-engineered E. coli mutant capable of quenching AI-2 quorum sensing (QS) system was utilized to evaluate the effect of AI-2 quenching on the anaerobic digestion of waste activated sludge (WAS) because the role of QS system via AI-2 in the process remains obscure. In this study, E. coli ∆luxS lsrR mutant cells were microencapsulated in sodium alginate beads and incubated with WAS anaerobically. After 15 days of anaerobic fermentation, the WAS containing double mutant cells produced significantly more methane than that of the parent E. coli cells. AI-2 quenching occurred concurrently with a shift of microbial communities that contribute to increasing acetate consumption by the Methanosarcina spp. resulting in an increase in methane production. KEY POINTS: • Impact of autoinducer 2 quenching in complex bacterial populations were determined. • Key microorganisms contributing to the increase of methane in WAS anaerobic digestion were found. • The AI-2 quenching is a potential regulatory in wastewater treatment and bioenergy research.
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18
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Bacterial Necromass Is Rapidly Metabolized by Heterotrophic Bacteria and Supports Multiple Trophic Levels of the Groundwater Microbiome. Microbiol Spectr 2022; 10:e0043722. [PMID: 35699474 PMCID: PMC9431026 DOI: 10.1128/spectrum.00437-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Pristine groundwater is a highly stable environment with microbes adapted to dark, oligotrophic conditions. Input events like heavy rainfalls can introduce the excess particulate organic matter, including surface-derived microorganisms, thereby disturbing the groundwater microbiome. Some surface-derived bacteria will not survive this translocation, leading to an input of necromass to the groundwater. Here, we investigated the effects of necromass addition to the microbial community in fractured bedrock groundwater, using groundwater mesocosms as model systems. We followed the uptake of 13C-labeled necromass by the bacterial and eukaryotic groundwater community quantitatively and over time using a complementary protein-stable and DNA-stable isotope probing approach. Necromass was rapidly depleted in the mesocosms within 4 days, accompanied by a strong decrease in Shannon diversity and a 10-fold increase in bacterial 16S rRNA gene copy numbers. Species of Flavobacterium, Massilia, Rheinheimera, Rhodoferax, and Undibacterium dominated the microbial community within 2 days and were identified as key players in necromass degradation, based on a 13C incorporation of >90% in their peptides. Their proteomes comprised various proteins for uptake and transport functions and amino acid metabolization. After 4 and 8 days, the autotrophic and mixotrophic taxa Nitrosomonas, Limnohabitans, Paucibacter, and Acidovorax increased in abundance with a 13C incorporation between 0.5% and 23%. Likewise, eukaryotes assimilated necromass-derived carbon either directly or indirectly. Our data point toward a fast and exclusive uptake of labeled necromass by a few specialists followed by a concerted action of groundwater microorganisms, including autotrophs presumably fueled by released, reduced nitrogen and sulfur compounds generated during necromass degradation. IMPORTANCE Subsurface microbiomes provide essential ecosystem services, like the generation of drinking water. These ecosystems are devoid of light-driven primary production, and microbial life is adapted to the resulting oligotrophic conditions. Modern groundwater is most vulnerable to anthropogenic and climatic impacts. Heavy rainfalls, which will increase with climate change, can result in high surface inputs into shallow aquifers by percolation or lateral flow. These inputs include terrestrial organic matter and surface-derived microbes that are not all capable to flourish in aquatic subsurface habitats. Here, we investigated the response of groundwater mesocosms to the addition of bacterial necromass, simulating event-driven surface input. We found that the groundwater microbiome responds with a rapid bloom of only a few primary degraders, followed by the activation of typical groundwater autotrophs and mixotrophs, as well as eukaryotes. Our results suggest that this multiphase strategy is essential to maintain the balance of the groundwater microbiome to provide ecosystem services.
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19
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Zahedi S, Gros M, Casabella O, Petrovic M, Balcazar JL, Pijuan M. Occurrence of veterinary drugs and resistance genes during anaerobic digestion of poultry and cattle manures. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 822:153477. [PMID: 35093343 DOI: 10.1016/j.scitotenv.2022.153477] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/24/2022] [Accepted: 01/24/2022] [Indexed: 06/14/2023]
Abstract
In the present paper, the mesophilic (35 °C) and thermophilic (55 °C) biomethanization of poultry and cattle manures were investigated using biochemical methane potential (BMP) tests. Specific methane production (SMP), 24 pharmaceutical compounds (PhACs), and five antibiotic resistance genes (ARGs) (blaKPC, ermB, qnrS, sul1 and tetW) together with the microbial community were analyzed. Mesophilic BMP tests resulted in the highest SMP when poultry manure was used (285.5 mL CH4/g VSS with poultry vs 239.6 mL CH4/g VSS with cattle manure) while thermophilic temperatures led to the highest SMP with cattle manure (231.2 mL CH4/g VSS with poultry vs 238.0 mL CH4/g VSS with cattle manure). Higher removals of veterinary pharmaceuticals were detected at 55 °C with both manures indicating that thermophilic digestion is better suited for the removal of these compounds. Tylosin, tilmicosin, chlortetracycline, and sulfamethoxazole presented removals higher than 50%, being the first two completely removed under mesophilic and thermophilic conditions. When comparing the relative abundance of ARGs at the end of each treatment, the most significant removal was found for qnrS which was not detected after the anaerobic treatment. The remaining ARGs did not suffer significant changes. Finally, microbial composition analysis showed that temperature affected the final microbial population more than the microorganisms present in the substrate or inoculum.
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Affiliation(s)
- Soraya Zahedi
- Catalan Institute for Water Research (ICRA), C. Emili Grahit 101, 17003 Girona, Spain; Universitat de Girona, Girona, Spain
| | - Meritxell Gros
- Catalan Institute for Water Research (ICRA), C. Emili Grahit 101, 17003 Girona, Spain; Universitat de Girona, Girona, Spain
| | - Oriol Casabella
- Catalan Institute for Water Research (ICRA), C. Emili Grahit 101, 17003 Girona, Spain; Universitat de Girona, Girona, Spain
| | - Mira Petrovic
- Catalan Institute for Water Research (ICRA), C. Emili Grahit 101, 17003 Girona, Spain; Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain
| | - Jose Luis Balcazar
- Catalan Institute for Water Research (ICRA), C. Emili Grahit 101, 17003 Girona, Spain; Universitat de Girona, Girona, Spain
| | - Maite Pijuan
- Catalan Institute for Water Research (ICRA), C. Emili Grahit 101, 17003 Girona, Spain; Universitat de Girona, Girona, Spain.
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20
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Zahedi S, Gros M, Petrović M, Balcazar JL, Pijuan M. Anaerobic treatment of swine manure under mesophilic and thermophilic temperatures: Fate of veterinary drugs and resistance genes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 818:151697. [PMID: 34793799 DOI: 10.1016/j.scitotenv.2021.151697] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/25/2021] [Accepted: 11/11/2021] [Indexed: 06/13/2023]
Abstract
The effect of anaerobic treatment of swine manure at 35 °C (mesophilic) and 55 °C (thermophilic) on methane production, microbial community and contaminants of emerging concern was investigated. Pasteurization pretreatment and post treatment was also investigated in combination with anaerobic treatment at 35 °C. Specific methane production (SMP), 26 pharmaceutical compounds (PhACs) and five antibiotic resistance genes (ARGs) (qnrS, tetW, ermB, sul1 and blaTEM) were evaluated. Mesophilic treatment resulted in the highest SMP regardless of whether pasteurization was applied. Marbofloxacin was the most abundant antibiotic in swine manure. In general, all groups of PhACs showed higher removals under thermophilic temperatures as compared to mesophilic. In general, pasteurization pretreatment followed by mesophilic anaerobic digestion provided the highest removals of ARGs. Finally, the genera Streptococcus, Clostridium and Pseudomonas which contain pathogenic species, were present in the swine manure. Streptococcus, which was the most abundant, was decreased during all the treatments, while the others only decreased under certain treatments.
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Affiliation(s)
- S Zahedi
- Catalan Institute for Water Research (ICRA), C. Emili Grahit 101, 17003 Girona, Spain; Universitat de Girona, Girona, Spain.
| | - M Gros
- Catalan Institute for Water Research (ICRA), C. Emili Grahit 101, 17003 Girona, Spain; Universitat de Girona, Girona, Spain
| | - M Petrović
- Catalan Institute for Water Research (ICRA), C. Emili Grahit 101, 17003 Girona, Spain; Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain
| | - J L Balcazar
- Catalan Institute for Water Research (ICRA), C. Emili Grahit 101, 17003 Girona, Spain; Universitat de Girona, Girona, Spain
| | - M Pijuan
- Catalan Institute for Water Research (ICRA), C. Emili Grahit 101, 17003 Girona, Spain; Universitat de Girona, Girona, Spain.
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21
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Thomson T, Fusi M, Bennett-Smith MF, Prinz N, Aylagas E, Carvalho S, Lovelock CE, Jones BH, Ellis JI. Contrasting Effects of Local Environmental and Biogeographic Factors on the Composition and Structure of Bacterial Communities in Arid Monospecific Mangrove Soils. Microbiol Spectr 2022; 10:e0090321. [PMID: 34985338 PMCID: PMC8729789 DOI: 10.1128/spectrum.00903-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 12/11/2021] [Indexed: 12/23/2022] Open
Abstract
Mangrove forests are important biotic sinks of atmospheric CO2 and play an integral role in nutrient-cycling and decontamination of coastal waters, thereby mitigating climatic and anthropogenic stressors. These services are primarily regulated by the activity of the soil microbiome. To understand how environmental changes may affect this vital part of the ecosystem, it is key to understand the patterns that drive microbial community assembly in mangrove forest soils. High-throughput amplicon sequencing (16S rRNA) was applied on samples from arid Avicennia marina forests across different spatial scales from local to regional. Alongside conventional analyses of community ecology, microbial co-occurrence networks were assessed to investigate differences in composition and structure of the bacterial community. The bacterial community composition varied more strongly along an intertidal gradient within each mangrove forest, than between forests in different geographic regions (Australia/Saudi Arabia). In contrast, co-occurrence networks differed primarily between geographic regions, illustrating that the structure of the bacterial community is not necessarily linked to its composition. The local diversity in mangrove forest soils may have important implications for the quantification of biogeochemical processes and is important to consider when planning restoration activities. IMPORTANCE Mangrove ecosystems are increasingly being recognized for their potential to sequester atmospheric carbon, thereby mitigating the effects of anthropogenically driven greenhouse gas emissions. The bacterial community in the soils plays an important role in the breakdown and recycling of carbon and other nutrients. To assess and predict changes in carbon storage, it is important to understand how the bacterial community is shaped by its environment. Here, we compared the bacterial communities of mangrove forests on different spatial scales, from local within-forest to biogeographic comparisons. The bacterial community composition differed more between distinct intertidal zones of the same forest than between forests in distant geographic regions. The calculated network structure of theoretically interacting bacteria, however, differed most between the geographic regions. Our findings highlight the importance of local environmental factors in shaping the microbial soil community in mangroves and highlight a disconnect between community composition and structure in microbial soil assemblages.
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Affiliation(s)
- T. Thomson
- University of Waikato, School of Science, Tauranga, New Zealand
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Saudi Arabia
| | - M. Fusi
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Saudi Arabia
- School of Applied Sciences, Edinburgh Napier University, Edinburgh, United Kingdom
| | - M. F. Bennett-Smith
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Saudi Arabia
| | - N. Prinz
- University of Waikato, School of Science, Tauranga, New Zealand
| | - E. Aylagas
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Saudi Arabia
| | - S. Carvalho
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Saudi Arabia
| | - C. E. Lovelock
- School of Biological Sciences, The University of Queensland, St Lucida, Australia
| | - B. H. Jones
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Saudi Arabia
| | - J. I. Ellis
- University of Waikato, School of Science, Tauranga, New Zealand
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Saudi Arabia
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22
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Fiard M, Cuny P, Sylvi L, Hubas C, Jézéquel R, Lamy D, Walcker R, El Houssainy A, Heimbürger-Boavida LE, Robinet T, Bihannic I, Gilbert F, Michaud E, Dirberg G, Militon C. Mangrove microbiota along the urban-to-rural gradient of the Cayenne estuary (French Guiana, South America): Drivers and potential bioindicators. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 807:150667. [PMID: 34599952 DOI: 10.1016/j.scitotenv.2021.150667] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 09/13/2021] [Accepted: 09/25/2021] [Indexed: 06/13/2023]
Abstract
The microbial communities inhabiting the Atlantic-East Pacific (AEP) mangroves have been poorly studied, and mostly comprise chronically polluted mangroves. In this study, we characterized changes in the structure and diversity of microbial communities of mangroves along the urban-to-rural gradient of the Cayenne estuary (French Guiana, South America) that experience low human impact. The microbial communities were assigned into 50 phyla. Proteobacteria, Chloroflexi, Acidobacteria, Bacteroidetes, and Planctomycetes were the most abundant taxa. The environmental determinants found to significantly correlated to the microbial communities at these mangroves were granulometry, dieldrin concentration, pH, and total carbon (TC) content. Furthermore, a precise analysis of the sediment highlights the existence of three types of anthropogenic pressure among the stations: (i) organic matter (OM) enrichment due to the proximity to the city and its wastewater treatment plant, (ii) dieldrin contamination, and (iii) naphthalene contamination. These forms of weak anthropogenic pressure seemed to impact the bacterial population size and microbial assemblages. A decrease in Bathyarchaeota, "Candidatus Nitrosopumilus", and Nitrospira genera was observed in mangroves subjected to OM enrichment. Mangroves polluted with organic contaminants were enriched in Desulfobacteraceae, Desulfarculaceae, and Acanthopleuribacteraceae (with dieldrin or polychlorobiphenyl contamination), and Chitinophagaceae and Geobacteraceae (with naphthalene contamination). These findings provide insights into the main environmental factors shaping microbial communities of mangroves in the AEP that experience low human impact and allow for the identification of several potential microbial bioindicators of weak anthropogenic pressure.
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Affiliation(s)
- Maud Fiard
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
| | - Philippe Cuny
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
| | - Léa Sylvi
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
| | - Cédric Hubas
- Biologie des Organismes et Ecosystèmes Aquatiques (UMR 8067 BOREA) Muséum National D'Histoire Naturelle, CNRS, Sorbonne Université, IRD, UCN, UA, Station Marine de Concarneau, 29900 Concarneau, France.
| | | | - Dominique Lamy
- Biologie des Organismes et Ecosystèmes Aquatiques (UMR 8067 BOREA) Muséum National D'Histoire Naturelle, CNRS, Sorbonne Université, IRD, UCN, UA, Rue Buffon, 75005 Paris, France; Institute of Ecology and Environmental Sciences of Paris (iEES-Paris), Sorbonne Université, Univ Paris Est Créteil, IRD, CNRS, INRA, 4 place Jussieu, 75005 Paris, France.
| | - Romain Walcker
- Laboratoire Ecologie Fonctionnelle et Environnement, Université de Toulouse, CNRS, Toulouse, France.
| | - Amonda El Houssainy
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
| | | | - Tony Robinet
- Biologie des Organismes et Ecosystèmes Aquatiques (UMR 8067 BOREA) Muséum National D'Histoire Naturelle, CNRS, Sorbonne Université, IRD, UCN, UA, Station Marine de Concarneau, 29900 Concarneau, France.
| | | | - Franck Gilbert
- Laboratoire Ecologie Fonctionnelle et Environnement, Université de Toulouse, CNRS, Toulouse, France.
| | - Emma Michaud
- Univ Brest, CNRS, IRD, Ifremer, LEMAR, 29280 Plouzané, France.
| | - Guillaume Dirberg
- Biologie des Organismes et Ecosystèmes Aquatiques (UMR 8067 BOREA) Muséum National D'Histoire Naturelle, CNRS, Sorbonne Université, IRD, UCN, UA, Rue Buffon, 75005 Paris, France.
| | - Cécile Militon
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
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23
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Bacteriome composition analysis of selected mineral water occurrences in Serbia. ARCH BIOL SCI 2022. [DOI: 10.2298/abs211223005s] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Bacterial metabarcoding analysis by 16S rDNA of five occurrences of mineral
waters in Serbia (Torda, Slankamen Banja, Lomnicki Kiseljak, Velika Vrbnica
and Obrenovacka Banja) indicated the presence of a high percentage of the
Proteobacteria phylum, followed by the Bacteroidetes phylum. The families
Rhodobacteraceae, Burkholderiaceae, Pseudomonadaceae, Methylophilaceae and
Moraxellaceae were the most dominant in the bacterial flora of the selected
occurrences, whereas the most represented genera were Acinetobacter,
Pseudorhodobacter, Pseudomonas, Limnohabitans, Massilia, Limnobacter and
Methylotenera. The presence of coliform bacteria was not detected. Alpha
diversity analysis revealed that Slankamen Banja and Lomnicki Kiseljak were
the richest of the selected occurrences, while the mineral waters of Torda,
Velika Vrbnica and Obrenovacka Banja were characterized by similar diversity
of bacterial communities determined by beta diversity analysis.
Physical-chemical analysis revealed the value of total dissolved solids
above 1 g/L, as well as elevated concentrations of some metals and
non-metals. The research concluded that specific bacteria contribute to the
development of biocorrosion and biofouling processes of water intake
facilities. In addition, some of these bacteria might be potential
indicators of the organic sources of pollution and/or biotechnological
natural remediators in the treatment of contaminated waters.
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24
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Bin Hudari MS, Vogt C, Richnow HH. Sulfidic acetate mineralization at 45°C by an aquifer microbial community: key players and effects of heat changes on activity and community structure. Environ Microbiol 2021; 24:370-389. [PMID: 34859568 DOI: 10.1111/1462-2920.15852] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 11/09/2021] [Accepted: 11/12/2021] [Indexed: 11/28/2022]
Abstract
High-Temperature Aquifer Thermal Energy Storage (HT-ATES) is a sustainable approach for integrating thermal energy from various sources into complex energy systems. Temperatures ≥45°C, which are relevant in impact zones of HT-ATES systems, may dramatically influence the structure and activities of indigenous aquifer microbial communities. Here, we characterized an acetate-mineralizing, sulfate-reducing microbial community derived from an aquifer and adapted to 45°C. Acetate mineralization was strongly inhibited at temperatures ≤25°C and 60°C. Prolonged incubation at 12°C and 25°C resulted in acetate mineralization recovery after 40-80 days whereas acetate was not mineralized at 60°C within 100 days. Cultures pre-grown at 45°C and inhibited for 28 days by incubation at 12°C, 25°C, or 60°C recovered quickly after changing the temperature back to 45°C. Phylotypes affiliated to the order Spirochaetales and to endospore-forming sulfate reducers of the order Clostridiales were highly abundant in microcosms being active at 45°C highlighting their key role. In summary, prolonged incubation at 45°C resulted in active microbial communities mainly consisting of organisms adapted to temperatures between the typical temperature range of mesophiles and thermophiles and being resilient to temporary heat changes.
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Affiliation(s)
- Mohammad S Bin Hudari
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Carsten Vogt
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Hans H Richnow
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
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25
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Vignale FA, Kurth D, Lencina AI, Poiré DG, Chihuailaf E, Muñoz-Herrera NC, Novoa F, Contreras M, Turjanski AG, Farías ME. Geobiology of Andean Microbial Ecosystems Discovered in Salar de Atacama, Chile. Front Microbiol 2021; 12:762076. [PMID: 34777316 PMCID: PMC8581658 DOI: 10.3389/fmicb.2021.762076] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 09/28/2021] [Indexed: 11/23/2022] Open
Abstract
The Salar de Atacama in the Chilean Central Andes harbors unique microbial ecosystems due to extreme environmental conditions, such as high altitude, low oxygen pressure, high solar radiation, and high salinity. Combining X-ray diffraction analyses, scanning electron microscopy and molecular diversity studies, we have characterized twenty previously unexplored Andean microbial ecosystems in eight different lakes and wetlands from the middle-east and south-east regions of this salt flat. The mats and microbialites studied are mainly formed by calcium carbonate (aragonite and calcite) and halite, whereas the endoevaporites are composed predominantly of gypsum and halite. The carbonate-rich mats and microbialites are dominated by Bacteroidetes and Proteobacteria phyla. Within the phylum Proteobacteria, the most abundant classes are Alphaproteobacteria, Gammaproteobacteria and Deltaproteobacteria. While in the phylum Bacteroidetes, the most abundant classes are Bacteroidia and Rhodothermia. Cyanobacteria, Chloroflexi, Planctomycetes, and Verrucomicrobia phyla are also well-represented in the majority of these systems. Gypsum endoevaporites, on the contrary, are dominated by Proteobacteria, Bacteroidetes, and Euryarchaeota phyla. The Cyanobacteria phylum is also abundant in these systems, but it is less represented in comparison to mats and microbialites. Regarding the eukaryotic taxa, diatoms are key structural components in most of the microbial ecosystems studied. The genera of diatoms identified were Achnanthes, Fallacia, Halamphora, Mastogloia, Navicula, Nitzschia, and Surirella. Normally, in the mats and microbialites, diatoms form nano-globular carbonate aggregates with filamentous cyanobacteria and other prokaryotic cells, suggesting their participation in the mineral precipitation process. This work expands our knowledge of the microbial ecosystems inhabiting the extreme environments from the Central Andes region, which is important to ensure their protection and conservation.
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Affiliation(s)
- Federico A. Vignale
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CCT, CONICET, San Miguel de Tucumán, Argentina
- Laboratorio de Bioinformática Estructural, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN)-CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Daniel Kurth
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CCT, CONICET, San Miguel de Tucumán, Argentina
| | - Agustina I. Lencina
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CCT, CONICET, San Miguel de Tucumán, Argentina
| | - Daniel G. Poiré
- Centro de Investigaciones Geológicas (CIG), Universidad Nacional de La Plata (UNLP)-CONICET, La Plata, Argentina
| | | | | | | | | | - Adrián G. Turjanski
- Laboratorio de Bioinformática Estructural, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN)-CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - María E. Farías
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CCT, CONICET, San Miguel de Tucumán, Argentina
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26
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Guo H, Zhang M, Chen Z, Shen Y, Lv J, Xu X, Yu H. The metabolic process of methane production by combined fermentation of coal and corn straw. BIORESOURCE TECHNOLOGY 2021; 337:125437. [PMID: 34320734 DOI: 10.1016/j.biortech.2021.125437] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/15/2021] [Accepted: 06/16/2021] [Indexed: 06/13/2023]
Abstract
The anaerobic degradation of coal combined with straw biomass can promote the methane production. The biogas production potential and metabolic pathway were explored via the co-digestion simulation experiment of coal and corn straw. The results showed that 2 g of corn straw combined respectively with 4 g of bituminous coal A, 6 g of bituminous coal B and 4 g of bituminous coal C resulted in highest methane yields. The structure of lignocellulose in corn straw was partially degraded into guaiacyl and syringyl units. Meanwhile, the content of biodegradable tyrosine like protein and soluble microbial by-products in liquid phase significantly decreased. Significantly, the structure of archaea altered from aceticlastic to hydrogenotrophic methanogens when the fermentation substrate changed from high to low rank coal. The proportion of hydrogenotrophic methanogens was significantly higher than that of aceticlastic and methylotrophic methanogens, and the hydrogenotrophic pathway was dominant than the aceticlastic pathway.
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Affiliation(s)
- Hongyu Guo
- School of Energy Science and Engineering, Henan Polytechnic University, Jiaozuo 454000, China; Collaborative Innovation Center of Coalbed Methane and Shale Gas for Central Plains Economic Region, Jiaozuo 454000, China.
| | - Minglu Zhang
- School of Energy Science and Engineering, Henan Polytechnic University, Jiaozuo 454000, China.
| | - Zhenhong Chen
- Research Institute of Petroleum Exploration & Development, Beijing 100083, China; China National Petroleum Corporation, Beijing 100083, China.
| | - Ye Shen
- Institute of Resources and Environment, Henan Polytechnic University, Jiaozuo 454000, China.
| | - Jinghui Lv
- College of Chemistry and Chemical Engineering, Henan Polytechnic University, Jiaozuo 454000, China.
| | - Xiaokai Xu
- School of Energy Science and Engineering, Henan Polytechnic University, Jiaozuo 454000, China.
| | - Hongfei Yu
- College of Chemistry and Chemical Engineering, Henan Polytechnic University, Jiaozuo 454000, China.
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27
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Rahlff J, Turzynski V, Esser SP, Monsees I, Bornemann TLV, Figueroa-Gonzalez PA, Schulz F, Woyke T, Klingl A, Moraru C, Probst AJ. Lytic archaeal viruses infect abundant primary producers in Earth's crust. Nat Commun 2021; 12:4642. [PMID: 34330907 PMCID: PMC8324899 DOI: 10.1038/s41467-021-24803-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 07/05/2021] [Indexed: 02/07/2023] Open
Abstract
The continental subsurface houses a major portion of life's abundance and diversity, yet little is known about viruses infecting microbes that reside there. Here, we use a combination of metagenomics and virus-targeted direct-geneFISH (virusFISH) to show that highly abundant carbon-fixing organisms of the uncultivated genus Candidatus Altiarchaeum are frequent targets of previously unrecognized viruses in the deep subsurface. Analysis of CRISPR spacer matches display resistances of Ca. Altiarchaea against eight predicted viral clades, which show genomic relatedness across continents but little similarity to previously identified viruses. Based on metagenomic information, we tag and image a putatively viral genome rich in protospacers using fluorescence microscopy. VirusFISH reveals a lytic lifestyle of the respective virus and challenges previous predictions that lysogeny prevails as the dominant viral lifestyle in the subsurface. CRISPR development over time and imaging of 18 samples from one subsurface ecosystem suggest a sophisticated interplay of viral diversification and adapting CRISPR-mediated resistances of Ca. Altiarchaeum. We conclude that infections of primary producers with lytic viruses followed by cell lysis potentially jump-start heterotrophic carbon cycling in these subsurface ecosystems.
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Affiliation(s)
- Janina Rahlff
- Department of Chemistry, Environmental Microbiology and Biotechnology (EMB), Group for Aquatic Microbial Ecology, University of Duisburg-Essen, Essen, Germany
- Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Victoria Turzynski
- Department of Chemistry, Environmental Microbiology and Biotechnology (EMB), Group for Aquatic Microbial Ecology, University of Duisburg-Essen, Essen, Germany
| | - Sarah P Esser
- Department of Chemistry, Environmental Microbiology and Biotechnology (EMB), Group for Aquatic Microbial Ecology, University of Duisburg-Essen, Essen, Germany
| | - Indra Monsees
- Department of Chemistry, Environmental Microbiology and Biotechnology (EMB), Group for Aquatic Microbial Ecology, University of Duisburg-Essen, Essen, Germany
| | - Till L V Bornemann
- Department of Chemistry, Environmental Microbiology and Biotechnology (EMB), Group for Aquatic Microbial Ecology, University of Duisburg-Essen, Essen, Germany
| | - Perla Abigail Figueroa-Gonzalez
- Department of Chemistry, Environmental Microbiology and Biotechnology (EMB), Group for Aquatic Microbial Ecology, University of Duisburg-Essen, Essen, Germany
| | | | - Tanja Woyke
- DOE Joint Genome Institute, Berkeley, CA, USA
| | - Andreas Klingl
- Plant Development & Electron Microscopy, Biocenter LMU Munich, Planegg-Martinsried, Germany
| | - Cristina Moraru
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl-von-Ossietzky-University Oldenburg, Oldenburg, Germany
| | - Alexander J Probst
- Department of Chemistry, Environmental Microbiology and Biotechnology (EMB), Group for Aquatic Microbial Ecology, University of Duisburg-Essen, Essen, Germany.
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28
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Cezar RM, Vezzani FM, Kaschuk G, Balsanelli E, de Souza EM, Vargas LK, Molin R. Crop rotation reduces the frequency of anaerobic soil bacteria in Red Latosol of Brazil. Braz J Microbiol 2021; 52:2169-2177. [PMID: 34319574 DOI: 10.1007/s42770-021-00578-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 07/11/2021] [Indexed: 10/20/2022] Open
Abstract
Crop diversity affects the processes of soil physical structuring and most likely provokes changes in the frequencies of soil microbial communities. The study was conducted for soil prokaryotic diversity sequencing 16S rDNA genes from a 25-year no-tillage experiment comprised of two crop systems: crop succession (Triticum aestivum-Glycine max) and rotation (Vicia sativa-Zea mays-Avena sativa-Glycine max-Triticum aestivum-Glycine max). The hypothesis was that a crop system with higher crop diversification (rotation) would affect the frequencies of prokaryotic taxa against a less diverse crop system (succession) altering the major soil functions guided by bacterial diversity. Soils in both crop systems were dominated by Proteobacteria (31%), Acidobacteria (23%), Actinobacteria (10%), and Gemmatimonadetes (7.2%), among other common copiotrophic soil bacteria. Crop systems did not affect the richness and diversity indexes of soil bacteria and soil archaea. However, the crop rotation system reduced only the frequencies of anaerobic metabolism bacteria Chloroacidobacteria, Holophagae, Spirochaetes, Euryarchaeota, and Crenarchaeota. It can be concluded that crop succession, a system that is poorer in root diversity over time, may have conditioned the soil to lower oxygen diffusion and built up ecological niches that suitable for anaerobic bacteria tolerating lower levels of oxygen. On the other hand, it appeared that crop rotation has restructured the soil over the years while enabling copiotrophic aerobic bacteria to dominate the soil ecosystem. The changes prompted by crop succession have implications for efficient soil organic matter decomposition, reduced greenhouse gas emissions, higher root activity, and overall soil productivity, which compromise to agriculture sustainability.
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Affiliation(s)
- Raul Matias Cezar
- Post-Graduate in Soil Science, Federal University of Paraná, Rua Dos Funcionários, 1540, Curitiba, PR, CEP 80035-050, Brazil
| | - Fabiane Machado Vezzani
- Post-Graduate in Soil Science, Federal University of Paraná, Rua Dos Funcionários, 1540, Curitiba, PR, CEP 80035-050, Brazil
| | - Glaciela Kaschuk
- Post-Graduate in Soil Science, Federal University of Paraná, Rua Dos Funcionários, 1540, Curitiba, PR, CEP 80035-050, Brazil.
| | - Eduardo Balsanelli
- Department of Biochemistry, Federal University of Paraná, Rua Francisco H. Dos Santos S/N, Curitiba, PR, CEP 81531-990, Brazil
| | - Emanuel Maltempi de Souza
- Department of Biochemistry, Federal University of Paraná, Rua Francisco H. Dos Santos S/N, Curitiba, PR, CEP 81531-990, Brazil
| | - Luciano Kayser Vargas
- Department of Agricultural Diagnosis and Research, Secretary of Agriculture and Livestock of the State of Rio Grande Do Sul, Rua Gonçalves Dias, 570, Porto Alegre, RS, CEP 90130-060, Brazil
| | - Rudimar Molin
- ABC Foundation, Rod. PR 151 km 288, Caixa-postal: 1003, Castro, PR, CEP 84165-700, Brazil
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29
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Mamet SD, Jimmo A, Conway A, Teymurazyan A, Talebitaher A, Papandreou Z, Chang YF, Shannon W, Peak D, Siciliano SD. Soil Buffering Capacity Can Be Used To Optimize Biostimulation of Psychrotrophic Hydrocarbon Remediation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:9864-9875. [PMID: 34170682 DOI: 10.1021/acs.est.1c01113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Effective bioremediation of hydrocarbons requires innovative approaches to minimize phosphate precipitation in soils of different buffering capacities. Understanding the mechanisms underlying sustained stimulation of bacterial activity remains a key challenge for optimizing bioremediation-particularly in northern regions. Positron emission tomography (PET) can trace microbial activity within the naturally occurring soil structure of intact soils. Here, we use PET to test two hypotheses: (1) optimizing phosphate bioavailability in soil will outperform a generic biostimulatory solution in promoting hydrocarbon remediation and (2) oligotrophic biostimulation will be more effective than eutrophic approaches. In so doing, we highlight the key bacterial taxa that underlie aerobic and anaerobic hydrocarbon degradation in subarctic soils. In particular, we showed that (i) optimized phosphate bioavailability outperformed generic biostimulatory solutions in promoting hydrocarbon degradation, (ii) oligotrophic biostimulation is more effective than eutrophic approaches, and (iii) optimized biostimulatory solutions stimulated specific soil regions and bacterial consortia. The knowledge gleaned from this study will be crucial in developing field-scale biodegradation treatments for sustained stimulation of bacterial activity in northern regions.
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Affiliation(s)
- Steven D Mamet
- College of Agriculture and Bioresources, Department of Soil Science, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5A8, Canada
| | - Amy Jimmo
- College of Agriculture and Bioresources, Department of Soil Science, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5A8, Canada
| | - Alexandra Conway
- College of Agriculture and Bioresources, Department of Soil Science, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5A8, Canada
| | - Aram Teymurazyan
- Department of Physics, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Alizera Talebitaher
- Department of Physics, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Zisis Papandreou
- Department of Physics, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Yu-Fen Chang
- Department of Physics, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
- Department of Mechanical and Marine Engineering, Western Norway University of Applied Sciences, Bergen 5063, Norway
- Nuclear Medicine and Radiation Biology Research Group, Department of Clinical Medicine, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Whitney Shannon
- College of Agriculture and Bioresources, Department of Soil Science, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5A8, Canada
- Department of Chemistry, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5C9, Canada
| | - Derek Peak
- College of Agriculture and Bioresources, Department of Soil Science, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5A8, Canada
| | - Steven D Siciliano
- College of Agriculture and Bioresources, Department of Soil Science, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5A8, Canada
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30
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Saha A, Mohapatra B, Kazy SK, Sar P. Variable response of arsenic contaminated groundwater microbial community to electron acceptor regime revealed by microcosm based high-throughput sequencing approach. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2021; 56:804-817. [PMID: 34284694 DOI: 10.1080/10934529.2021.1930448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 05/10/2021] [Accepted: 05/11/2021] [Indexed: 06/13/2023]
Abstract
Arsenic (As) mobilization in alluvial aquifers is facilitated by microbially catalyzed redox transformations that depend on the availability of electron acceptors (EAs). In this study, the response of an As-contaminated groundwater microbial community from West Bengal, India towards varied EAs was elucidated through microcosm based 16S rRNA gene amplicon sequencing. Acinetobacter, Deinococcus, Nocardioides, etc., and several unclassified bacteria (Ignavibacteria) and archaea (Bathyarchaeia, Micrarchaeia) previously not reported from As-contaminated groundwater of West Bengal, characterized the groundwater community. Distinct shifts in community composition were observed in response to various EAs. Enrichment of operational taxonomic units (OTUs) affiliated to Denitratisoma (NO3-), Spirochaetaceae (Mn4+), Deinococcus (As5+), Ruminiclostridium (Fe3+), Macellibacteroides (SO42-), Holophagae-Subgroup 7 (HCO3-), Dechloromonas and Geobacter (EA mixture) was noted. Alternatively, As3+ amendment as electron donor allowed predominance of Rhizobium. Taxonomy based functional profiling highlighted the role of chemoorganoheterotrophs capable of concurrent reduction of NO3-, Fe3+, SO42-, and As biotransformation in As-contaminated groundwater of West Bengal. Our analysis revealed two major aspects of the community, (a) taxa selective toward responding to the EAs, and (b) multifaceted nature of taxa appearing in abundance in response to multiple substrates. Thus, the results emphasized the potential of microbial community members to influence the biogeochemical cycling of As and other dominant anions/cations.
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Affiliation(s)
- Anumeha Saha
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
| | - Balaram Mohapatra
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
| | - Sufia Khannam Kazy
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, West Bengal, India
| | - Pinaki Sar
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
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31
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Pavlovska M, Prekrasna I, Dykyi E, Zotov A, Dzhulai A, Frolova A, Slobodnik J, Stoica E. Niche partitioning of bacterial communities along the stratified water column in the Black Sea. Microbiologyopen 2021; 10:e1195. [PMID: 34180601 PMCID: PMC8217838 DOI: 10.1002/mbo3.1195] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 04/21/2021] [Accepted: 04/21/2021] [Indexed: 11/22/2022] Open
Abstract
The Black Sea is the largest semi‐closed permanently anoxic basin on our planet with long‐term stratification. The study aimed at describing the Black Sea microbial community taxonomic and functional composition within the range of depths spanning across oxic/anoxic interface, and to uncover the factors behind both their vertical and regional differentiation. 16S rRNA gene MiSeq sequencing was applied to get the data on microbial community taxonomy, and the PICRUSt pipeline was used to infer their functional profile. The normoxic zone was mainly inhabited by primary producers and heterotrophic prokaryotes (e.g., Flavobacteriaceae, Rhodobacteraceae, Synechococcaceae) whereas the euxinic zone—by heterotrophic and chemoautotrophic taxa (e.g., MSBL2, Piscirickettsiaceae, and Desulfarculaceae). Assimilatory sulfate reduction and oxygenic photosynthesis were prevailing within the normoxic zone, while the role of nitrification, dissimilatory sulfate reduction, and anoxygenic photosynthesis increased in the oxygen‐depleted water column part. Regional differentiation of microbial communities between the Ukrainian shelf and offshore zone was detected as well, yet it was significantly less pronounced than the vertical one. It is suggested that regional differentiation within a well‐oxygenated zone is driven by the difference in phytoplankton communities providing various substrates for the prokaryotes, whereas redox stratification is the main driving force behind microbial community vertical structure.
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Affiliation(s)
- Mariia Pavlovska
- State Institution National Antarctic Scientific Center, Kyiv, Ukraine.,Ukrainian Scientific Center of Ecology of the Sea, Odesa, Ukraine.,National University of Life and Environmental Sciences of Ukraine, Kyiv, Ukraine
| | | | - Evgen Dykyi
- State Institution National Antarctic Scientific Center, Kyiv, Ukraine.,Ukrainian Scientific Center of Ecology of the Sea, Odesa, Ukraine
| | - Andrii Zotov
- State Institution National Antarctic Scientific Center, Kyiv, Ukraine.,State Institution Institute of Marine Biology of the NAS of Ukraine, Odesa, Ukraine
| | - Artem Dzhulai
- State Institution National Antarctic Scientific Center, Kyiv, Ukraine
| | - Alina Frolova
- Institute of Molecular Biology and Genetics of NASU, Kyiv, Ukraine
| | | | - Elena Stoica
- National Institute for Marine Research and Development "Grigore Antipa", Constanta, Romania
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32
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Toth CRA, Luo F, Bawa N, Webb J, Guo S, Dworatzek S, Edwards EA. Anaerobic Benzene Biodegradation Linked to the Growth of Highly Specific Bacterial Clades. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:7970-7980. [PMID: 34041904 DOI: 10.1021/acs.est.1c00508] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Reliance on bioremediation to remove benzene from anoxic environments has proven risky for decades but for unknown reasons. Research has revealed a strong link between anaerobic benzene biodegradation and the enrichment of highly specific microbes, including Thermincola in the family Peptococcaceae and the deltaproteobacterial Candidate Sva0485 clade. Using aquifer materials from Canadian Forces Base Borden, we compared five bioremediation approaches in batch microcosms. Under conditions simulating natural attenuation or sulfate biostimulation, benzene was not degraded after 1-2 years of incubation and no enrichment of known benzene-degrading microbes occurred. In contrast, nitrate-amended microcosms reported benzene biodegradation coincident with significant growth of Thermincola spp., along with a functional gene presumed to catalyze anaerobic benzene carboxylation (abcA). Inoculation with 2.5% of a methanogenic benzene-degrading consortium containing Sva0485 (Deltaproteobacteria ORM2) resulted in benzene biodegradation in the presence of sulfate or under methanogenic conditions. The presence of other hydrocarbon co-contaminants decreased the rates of benzene degradation by a factor of 2 to 4. Tracking the abundance of the abcA gene and 16S rRNA genes specific for benzene-degrading Thermincola and Sva0485 is recommended to monitor benzene bioremediation in anoxic groundwater systems to further uncover growth-rate-limiting conditions for these two intriguing phylotypes.
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Affiliation(s)
- Courtney R A Toth
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - Fei Luo
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - Nancy Bawa
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - Jennifer Webb
- SiREM, 130 Stone Road West, Guelph, Ontario N1G 3Z2, Canada
| | - Shen Guo
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | | | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
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33
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Nguyen TT, Paulsen JE, Landfald B. Seafloor deposition of water-based drill cuttings generates distinctive and lengthy sediment bacterial community changes. MARINE POLLUTION BULLETIN 2021; 164:111987. [PMID: 33515825 DOI: 10.1016/j.marpolbul.2021.111987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 12/21/2020] [Accepted: 12/22/2020] [Indexed: 06/12/2023]
Abstract
The spatial extent and persistence of bacterial change caused by deposition of water-based drill cuttings on the seafloor were explored by a community-wide approach. Ten centimeter sediment cores were sampled along transects extending from ≤15 m to 250 m from three nearby drilling sites in the southern Barents Sea. Eight months, 8 years and 15 years, respectively, had passed since the completion of the drillings. At locations heavily affected by drill cuttings, the two most recent sites showed distinct, corresponding deviances from native Barents Sea bacterial community profiles. Otherwise marginal groups, including Mollicutes and Clostridia, showed significant increases in relative abundance. Beyond 100 m from the boreholes the microbiotas appeared undisturbed, as they did at any distance from the 15-years old borehole. The extent of the biological distortion, as indicated by the present microbial study, agreed with previously published macrofaunal surveys at the same drilling sites.
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Affiliation(s)
- Tan T Nguyen
- Norwegian College of Fishery Science, UiT The Arctic University of Norway, PO Box 6050 Langnes, 9037 Tromsø, Norway.
| | | | - Bjarne Landfald
- Norwegian College of Fishery Science, UiT The Arctic University of Norway, PO Box 6050 Langnes, 9037 Tromsø, Norway.
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34
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Jokanović S, Kajan K, Perović S, Ivanić M, Mačić V, Orlić S. Anthropogenic influence on the environmental health along Montenegro coast based on the bacterial and chemical characterization. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 271:116383. [PMID: 33387780 DOI: 10.1016/j.envpol.2020.116383] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 12/15/2020] [Accepted: 12/22/2020] [Indexed: 06/12/2023]
Abstract
Coastal marine sediments are particularly exposed to human activities. The function of a coastal ecosystem is largely affected by eutrophication, wastewater discharges, chemical pollution, port activities, industry and tourism. Bacterial classification can be used as a measure in assessing the harmful effects on the ecosystem. This study provided insight into the environmental health of the coastal region of Montenegro analyzing the possible impact of PAHs and PCBs upon the bacterial community diversity and function as well as nutrients. Two stations at the shipyards were defined as very high PAH polluted together with PCB concentration exceeding threshold values. The bacterial community at the OTU level clustered together all stations except the most polluted site (SBL), the main tourist destination in Montenegro (BDV) and the estuary site (ADB) forming the independent clusters. Bacterial community based on the OTU level was driven by PAHs, TOC and silt content. The lowest richness and diversity were indicated at the site with the highest concentration of PAHs and PCBs with the highest abundance of Alphaproteobacteria followed by Gammaproteobacteria. OTUs affiliated to phyla BRC1, Dadabacteria and Spirochaetes were present with a total abundance higher than 1% only at the most polluted site indicating their persistence and possible potential for degradation of aromatic compounds. To compare functional capabilities potentially related to biodegradation of aromatic compounds and active transport systems, PICRUSt was used to predict metagenomes of the sediments. From our data, we identified specific bacterial community and predicted metabolic pathways that give us a picture of the environmental health along the coast of Montenegro, which provides us a new insight into human-induced pollution impacts on the coastal ecosystem.
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Affiliation(s)
- Sandra Jokanović
- Institute of Marine Biology, University of Montenegro, 85 330, Kotor, Montenegro
| | - Katarina Kajan
- Ruđer Bošković Institute, Division of Materials Chemistry, 10 000, Zagreb, Croatia; Center of Excellence for Science and Technology-Integration of Mediterranean Region (STIM), University of Split, 21 000, Split, Croatia
| | - Svetlana Perović
- Faculty of Science and Mathematics, University of Montenegro, 81 000, Podgorica, Montenegro
| | - Maja Ivanić
- Ruđer Bošković Institute, Division for Marine and Environmental Research, 10 000, Zagreb, Croatia
| | - Vesna Mačić
- Institute of Marine Biology, University of Montenegro, 85 330, Kotor, Montenegro
| | - Sandi Orlić
- Ruđer Bošković Institute, Division of Materials Chemistry, 10 000, Zagreb, Croatia; Center of Excellence for Science and Technology-Integration of Mediterranean Region (STIM), University of Split, 21 000, Split, Croatia.
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35
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Bin Hudari MS, Vogt C, Richnow HH. Effect of Temperature on Acetate Mineralization Kinetics and Microbial Community Composition in a Hydrocarbon-Affected Microbial Community During a Shift From Oxic to Sulfidogenic Conditions. Front Microbiol 2021; 11:606565. [PMID: 33391229 PMCID: PMC7773710 DOI: 10.3389/fmicb.2020.606565] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 11/23/2020] [Indexed: 01/04/2023] Open
Abstract
Aquifer thermal energy storage (ATES) allows for the seasonal storage and extraction of heat in the subsurface thus reducing reliance on fossil fuels and supporting decarbonization of the heating and cooling sector. However, the impacts of higher temperatures toward biodiversity and ecosystem services in the subsurface environment remain unclear. Here, we conducted a laboratory microcosm study comprising a hydrocarbon-degrading microbial community from a sulfidic hydrocarbon-contaminated aquifer spiked with 13C-labeled acetate and incubated at temperatures between 12 and 80°C to evaluate (i) the extent and rates of acetate mineralization and (ii) the resultant temperature-induced shifts in the microbial community structure. We observed biphasic mineralization curves at 12, 25, 38, and 45°C, arising from immediate and fast aerobic mineralization due to an initial oxygen exposure, followed by slower mineralization at sulfidogenic conditions. At 60°C and several replicates at 45°C, acetate was only aerobically mineralized. At 80°C, no mineralization was observed within 178 days. Rates of acetate mineralization coupled to sulfate reduction at 25 and 38°C were six times faster than at 12°C. Distinct microbial communities developed in oxic and strictly anoxic phases of mineralization as well as at different temperatures. Members of the Alphaproteobacteria were dominant in the oxic mineralization phase at 12–38°C, succeeded by a more diverse community in the anoxic phase composed of Deltaproteobacteria, Clostridia, Spirochaetia, Gammaproteobacteria and Anaerolinea, with varying abundances dependent on the temperature. In the oxic phases at 45 and 60°C, phylotypes affiliated to spore-forming Bacilli developed. In conclusion, temperatures up to 38°C allowed aerobic and anaerobic acetate mineralization albeit at varying rates, while mineralization occurred mainly aerobically between 45 and 60°C; thermophilic sulfate reducers being active at temperatures > 45°C were not detected. Hence, temperature may affect dissolved organic carbon mineralization rates in ATES while the variability in the microbial community composition during the transition from micro-oxic to sulfidogenic conditions highlights the crucial role of electron acceptor availability when combining ATES with bioremediation.
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Affiliation(s)
| | - Carsten Vogt
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Hans Hermann Richnow
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research, Leipzig, Germany
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36
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Park H, Patel A, Hunt KA, Henson MA, Carlson RP. Artificial consortium demonstrates emergent properties of enhanced cellulosic-sugar degradation and biofuel synthesis. NPJ Biofilms Microbiomes 2020; 6:59. [PMID: 33268782 PMCID: PMC7710750 DOI: 10.1038/s41522-020-00170-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 10/23/2020] [Indexed: 01/03/2023] Open
Abstract
Planktonic cultures, of a rationally designed consortium, demonstrated emergent properties that exceeded the sums of monoculture properties, including a >200% increase in cellobiose catabolism, a >100% increase in glycerol catabolism, a >800% increase in ethanol production, and a >120% increase in biomass productivity. The consortium was designed to have a primary and secondary-resource specialist that used crossfeeding with a positive feedback mechanism, division of labor, and nutrient and energy transfer via necromass catabolism. The primary resource specialist was Clostridium phytofermentans (a.k.a. Lachnoclostridium phytofermentans), a cellulolytic, obligate anaerobe. The secondary-resource specialist was Escherichia coli, a versatile, facultative anaerobe, which can ferment glycerol and byproducts of cellobiose catabolism. The consortium also demonstrated emergent properties of enhanced biomass accumulation when grown as biofilms, which created high cell density communities with gradients of species along the vertical axis. Consortium biofilms were robust to oxic perturbations with E. coli consuming O2, creating an anoxic environment for C. phytofermentans. Anoxic/oxic cycling further enhanced biomass productivity of the biofilm consortium, increasing biomass accumulation ~250% over the sum of the monoculture biofilms. Consortium emergent properties were credited to several synergistic mechanisms. E. coli consumed inhibitory byproducts from cellobiose catabolism, driving higher C. phytofermentans growth and higher cellulolytic enzyme production, which in turn provided more substrate for E. coli. E. coli necromass enhanced C. phytofermentans growth while C. phytofermentans necromass aided E. coli growth via the release of peptides and amino acids, respectively. In aggregate, temporal cycling of necromass constituents increased flux of cellulose-derived resources through the consortium. The study establishes a consortia-based, bioprocessing strategy built on naturally occurring interactions for improved conversion of cellulose-derived sugars into bioproducts.
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Affiliation(s)
- Heejoon Park
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, USA.,Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA.,Department of Engineering and Technology, University of North Alabama, Florence, AL, USA
| | - Ayushi Patel
- Department of Chemical Engineering and Institute for Applied Life Sciences, University of Massachusetts, Amherst, MA, USA
| | - Kristopher A Hunt
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, USA.,Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA.,Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Michael A Henson
- Department of Chemical Engineering and Institute for Applied Life Sciences, University of Massachusetts, Amherst, MA, USA
| | - Ross P Carlson
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, USA. .,Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA.
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37
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Dong X, Rattray JE, Campbell DC, Webb J, Chakraborty A, Adebayo O, Matthews S, Li C, Fowler M, Morrison NM, MacDonald A, Groves RA, Lewis IA, Wang SH, Mayumi D, Greening C, Hubert CRJ. Thermogenic hydrocarbon biodegradation by diverse depth-stratified microbial populations at a Scotian Basin cold seep. Nat Commun 2020; 11:5825. [PMID: 33203858 PMCID: PMC7673041 DOI: 10.1038/s41467-020-19648-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 10/06/2020] [Indexed: 11/08/2022] Open
Abstract
At marine cold seeps, gaseous and liquid hydrocarbons migrate from deep subsurface origins to the sediment-water interface. Cold seep sediments are known to host taxonomically diverse microorganisms, but little is known about their metabolic potential and depth distribution in relation to hydrocarbon and electron acceptor availability. Here we combined geophysical, geochemical, metagenomic and metabolomic measurements to profile microbial activities at a newly discovered cold seep in the deep sea. Metagenomic profiling revealed compositional and functional differentiation between near-surface sediments and deeper subsurface layers. In both sulfate-rich and sulfate-depleted depths, various archaeal and bacterial community members are actively oxidizing thermogenic hydrocarbons anaerobically. Depth distributions of hydrocarbon-oxidizing archaea revealed that they are not necessarily associated with sulfate reduction, which is especially surprising for anaerobic ethane and butane oxidizers. Overall, these findings link subseafloor microbiomes to various biochemical mechanisms for the anaerobic degradation of deeply-sourced thermogenic hydrocarbons.
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Affiliation(s)
- Xiyang Dong
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China.
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada.
| | - Jayne E Rattray
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - D Calvin Campbell
- Geological Survey of Canada-Atlantic, Dartmouth, NS, B3B 1A6, Canada
| | - Jamie Webb
- Applied Petroleum Technology (Canada), Calgary, AB, T2N 1Z6, Canada
| | - Anirban Chakraborty
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Oyeboade Adebayo
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Stuart Matthews
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Carmen Li
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Martin Fowler
- Applied Petroleum Technology (Canada), Calgary, AB, T2N 1Z6, Canada
| | - Natasha M Morrison
- Nova Scotia Department of Energy and Mines, Halifax, NS, B2Y 4A2, Canada
| | - Adam MacDonald
- Nova Scotia Department of Energy and Mines, Halifax, NS, B2Y 4A2, Canada
| | - Ryan A Groves
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Ian A Lewis
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Scott H Wang
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Daisuke Mayumi
- Institute for Geo-Resources and Environment, Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, 305-8567, Japan
| | - Chris Greening
- School of Biological Sciences, Monash University, Clayton, VIC, 3800, Australia
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Casey R J Hubert
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada.
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38
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Quaiyum S, Igarashi K, Narihiro T, Kato S. Microbial Community Analysis of Anaerobic Enrichment Cultures Supplemented with Bacterial Peptidoglycan as the Sole Substrate. Microbes Environ 2020; 35. [PMID: 32921647 PMCID: PMC7511781 DOI: 10.1264/jsme2.me20002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Methanogenic microbial communities were enriched from rice paddy soil and anaerobic digester sludge using peptidoglycan purified from gram-negative Escherichia coli or gram-positive Micrococcus luteus as the sole substrate. Methane production data suggested the anaerobic degradation of peptidoglycan and also that peptidoglycan from E. coli had lower degradability. The community structures of enrichment cultures fed peptidoglycan from E. coli or M. luteus were similar, but distinctly different. A number of phylogenetically novel and uncultured bacteria, particularly in the phyla Bacteroidetes, WWE1, Armatimonadetes, and Verrucomicrobia, dominated the enrichment cultures, suggesting their involvement in anaerobic peptidoglycan degradation.
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Affiliation(s)
- Samia Quaiyum
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University.,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology
| | - Kensuke Igarashi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology
| | - Takashi Narihiro
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology
| | - Souichiro Kato
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University.,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology
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39
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Karnachuk OV, Lukina AP, Kadnikov VV, Sherbakova VA, Beletsky AV, Mardanov AV, Ravin NV. Targeted isolation based on metagenome‐assembled genomes reveals a phylogenetically distinct group of thermophilic spirochetes from deep biosphere. Environ Microbiol 2020; 23:3585-3598. [DOI: 10.1111/1462-2920.15218] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/18/2020] [Accepted: 08/27/2020] [Indexed: 12/22/2022]
Affiliation(s)
| | | | - Vitaly V. Kadnikov
- Institute of Bioengineering Research Center of Biotechnology of the Russian Academy of Sciences Moscow 119071 Russia
| | - Viktoria A. Sherbakova
- Skryabin Institute of Biochemistry and Physiology of Microorganisms Federal Research Center ‘Pushchino Scientific Center for Biological Research, Russian Academy of Sciences’ Pushchino Moscow 142290 Russia
| | - Alexey V. Beletsky
- Institute of Bioengineering Research Center of Biotechnology of the Russian Academy of Sciences Moscow 119071 Russia
| | - Andrey V. Mardanov
- Institute of Bioengineering Research Center of Biotechnology of the Russian Academy of Sciences Moscow 119071 Russia
| | - Nikolai V. Ravin
- Institute of Bioengineering Research Center of Biotechnology of the Russian Academy of Sciences Moscow 119071 Russia
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40
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Tamburini E, Doni L, Lussu R, Meloni F, Cappai G, Carucci A, Casalone E, Mastromei G, Vitali F. Impacts of Anthropogenic Pollutants on Benthic Prokaryotic Communities in Mediterranean Touristic Ports. Front Microbiol 2020; 11:1234. [PMID: 32655521 PMCID: PMC7326019 DOI: 10.3389/fmicb.2020.01234] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 05/14/2020] [Indexed: 02/04/2023] Open
Abstract
Ports and marinas are central nodes in transport network and play a strategic role in coastal development. They receive pollution from land-based sources, marine traffic and port infrastructures on one side and constitute a potential pollution source for the adjacent coastal areas on the other. The aim of the present study was to evaluate the effects of organic and inorganic co-contamination on the prokaryotic communities in sediments from three Mediterranean ports. The structure and composition of the bacterial and archaeal communities were assessed by targeted metagenomic analysis of the 16S rRNA gene, and the links of prokaryotic communities with environmental and pollution variables were investigated. The harbors presented pronounced site-specificity in the environmental properties and pollution status. Consistently, the structure of archaeal and bacterial communities in surface sediments exhibited a strong spatial variation among the three investigated ports. On the contrary, a wide overlap in composition of prokaryotic assemblages among sites was found, but local variation in the community composition and loss of prokaryotic diversity was highlighted in a heavily impacted port sector near a shipyard. We provided evidences that organic matter, metals and PAHs as well as temperature and salinity play a strong role in structuring benthic bacterial communities significantly contributing to the understanding of their responses to anthropogenic perturbations in marine coastal areas. Among metals, copper was recognized as strongly associated with the observed changes in bacterial assemblages. Overall, this study provides the first assessment of the effects exerted by multiple organic and inorganic contaminations on benthic prokaryotes in ports over a large spatial scale and designates bacterial community as a candidate tool for the monitoring of the sediment quality status in harbors.
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Affiliation(s)
- Elena Tamburini
- Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Lapo Doni
- Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy.,Department of Biology, University of Florence, Florence, Italy
| | - Raffaela Lussu
- Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Federico Meloni
- Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Giovanna Cappai
- Department of Civil-Environmental Engineering and Architecture, University of Cagliari, Cagliari, Italy
| | - Alessandra Carucci
- Department of Civil-Environmental Engineering and Architecture, University of Cagliari, Cagliari, Italy
| | - Enrico Casalone
- Department of Biology, University of Florence, Florence, Italy
| | | | - Francesco Vitali
- Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy.,Institute of Agricultural Biology and Biotechnology, National Research Council, Pisa, Italy
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41
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Hanajima D, Aoyagi T, Hori T. Dead bacterial biomass-assimilating bacterial populations in compost revealed by high-sensitivity stable isotope probing. ENVIRONMENT INTERNATIONAL 2019; 133:105235. [PMID: 31675570 DOI: 10.1016/j.envint.2019.105235] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 09/30/2019] [Accepted: 09/30/2019] [Indexed: 06/10/2023]
Abstract
Pathogens are known to survive in compost and to regrow under the influence of certain factors, such as moisture content, temperature and nutrient availability. Dead biomass, by providing available nutrients, is a factor that may affect pathogen regrowth. However, the indigenous microorganisms, including pathogens, that grown on the dead biomass of compost have not yet been identified. Here, the regrowth potential of the pathogenic indicator bacterium Escherichia coli in the presence of dead bacterial biomass was determined, and the biomass metabolizers that grew competitively with E. coli were identified by high-sensitivity stable isotope probing of rRNA. Culture-dependent analysis indicated that the addition of dead bacterial biomass did not stimulate E. coli growth. High-throughput analysis of density-resolved 16S rRNA molecules from compost samples amended with carbon-13-labeled dead bacterial biomass revealed dead bacterial-assimilating bacteria, including Sphingobium sp., myxobacterial lineages and Bacillales. These bacteria are potentially competitive with pathogens due to their preferential assimilation of dead biomass in compost.
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Affiliation(s)
- Dai Hanajima
- Dairy Research Division, Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization (NARO), 1 Hitsujigaoka, Toyohira, Sapporo 062-8555, Japan.
| | - Tomo Aoyagi
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba 305-8569, Japan
| | - Tomoyuki Hori
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba 305-8569, Japan
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42
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Greening C, Geier R, Wang C, Woods LC, Morales SE, McDonald MJ, Rushton-Green R, Morgan XC, Koike S, Leahy SC, Kelly WJ, Cann I, Attwood GT, Cook GM, Mackie RI. Diverse hydrogen production and consumption pathways influence methane production in ruminants. ISME JOURNAL 2019; 13:2617-2632. [PMID: 31243332 PMCID: PMC6776011 DOI: 10.1038/s41396-019-0464-2] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 06/03/2019] [Accepted: 06/07/2019] [Indexed: 01/17/2023]
Abstract
Farmed ruminants are the largest source of anthropogenic methane emissions globally. The methanogenic archaea responsible for these emissions use molecular hydrogen (H2), produced during bacterial and eukaryotic carbohydrate fermentation, as their primary energy source. In this work, we used comparative genomic, metatranscriptomic and co-culture-based approaches to gain a system-wide understanding of the organisms and pathways responsible for ruminal H2 metabolism. Two-thirds of sequenced rumen bacterial and archaeal genomes encode enzymes that catalyse H2 production or consumption, including 26 distinct hydrogenase subgroups. Metatranscriptomic analysis confirmed that these hydrogenases are differentially expressed in sheep rumen. Electron-bifurcating [FeFe]-hydrogenases from carbohydrate-fermenting Clostridia (e.g., Ruminococcus) accounted for half of all hydrogenase transcripts. Various H2 uptake pathways were also expressed, including methanogenesis (Methanobrevibacter), fumarate and nitrite reduction (Selenomonas), and acetogenesis (Blautia). Whereas methanogenesis-related transcripts predominated in high methane yield sheep, alternative uptake pathways were significantly upregulated in low methane yield sheep. Complementing these findings, we observed significant differential expression and activity of the hydrogenases of the hydrogenogenic cellulose fermenter Ruminococcus albus and the hydrogenotrophic fumarate reducer Wolinella succinogenes in co-culture compared with pure culture. We conclude that H2 metabolism is a more complex and widespread trait among rumen microorganisms than previously recognised. There is evidence that alternative hydrogenotrophs, including acetogenic and respiratory bacteria, can prosper in the rumen and effectively compete with methanogens for H2. These findings may help to inform ongoing strategies to mitigate methane emissions by increasing flux through alternative H2 uptake pathways, including through animal selection, dietary supplementation and methanogenesis inhibitors.
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Affiliation(s)
- Chris Greening
- School of Biological Sciences, Monash University, Clayton, VIC, 3800, Australia.
| | - Renae Geier
- Department of Animal Sciences and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Cecilia Wang
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
| | - Laura C Woods
- School of Biological Sciences, Monash University, Clayton, VIC, 3800, Australia
| | - Sergio E Morales
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
| | - Michael J McDonald
- School of Biological Sciences, Monash University, Clayton, VIC, 3800, Australia
| | - Rowena Rushton-Green
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
| | - Xochitl C Morgan
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
| | - Satoshi Koike
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Sinead C Leahy
- Grasslands Research Centre, AgResearch Ltd., Palmerston North, 4410, New Zealand
| | | | - Isaac Cann
- Department of Animal Sciences and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Graeme T Attwood
- Grasslands Research Centre, AgResearch Ltd., Palmerston North, 4410, New Zealand
| | - Gregory M Cook
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
| | - Roderick I Mackie
- Department of Animal Sciences and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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43
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Piché-Choquette S, Constant P. Molecular Hydrogen, a Neglected Key Driver of Soil Biogeochemical Processes. Appl Environ Microbiol 2019; 85:e02418-18. [PMID: 30658976 PMCID: PMC6414374 DOI: 10.1128/aem.02418-18] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The atmosphere of the early Earth is hypothesized to have been rich in reducing gases such as hydrogen (H2). H2 has been proposed as the first electron donor leading to ATP synthesis due to its ubiquity throughout the biosphere as well as its ability to easily diffuse through microbial cells and its low activation energy requirement. Even today, hydrogenase enzymes enabling the production and oxidation of H2 are found in thousands of genomes spanning the three domains of life across aquatic, terrestrial, and even host-associated ecosystems. Even though H2 has already been proposed as a universal growth and maintenance energy source, its potential contribution as a driver of biogeochemical cycles has received little attention. Here, we bridge this knowledge gap by providing an overview of the classification, distribution, and physiological role of hydrogenases. Distribution of these enzymes in various microbial functional groups and recent experimental evidence are finally integrated to support the hypothesis that H2-oxidizing microbes are keystone species driving C cycling along O2 concentration gradients found in H2-rich soil ecosystems. In conclusion, we suggest focusing on the metabolic flexibility of H2-oxidizing microbes by combining community-level and individual-level approaches aiming to decipher the impact of H2 on C cycling and the C-cycling potential of H2-oxidizing microbes, via both culture-dependent and culture-independent methods, to give us more insight into the role of H2 as a driver of biogeochemical processes.
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44
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Kessler AJ, Chen YJ, Waite DW, Hutchinson T, Koh S, Popa ME, Beardall J, Hugenholtz P, Cook PLM, Greening C. Bacterial fermentation and respiration processes are uncoupled in anoxic permeable sediments. Nat Microbiol 2019; 4:1014-1023. [DOI: 10.1038/s41564-019-0391-z] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 01/28/2019] [Indexed: 11/09/2022]
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Kraiselburd I, Brüls T, Heilmann G, Kaschani F, Kaiser M, Meckenstock RU. Metabolic reconstruction of the genome of candidate Desulfatiglans TRIP_1 and identification of key candidate enzymes for anaerobic phenanthrene degradation. Environ Microbiol 2019; 21:1267-1286. [PMID: 30680888 PMCID: PMC6849830 DOI: 10.1111/1462-2920.14527] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 12/12/2018] [Indexed: 11/30/2022]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are widely distributed pollutants. As oxygen is rapidly depleted in water‐saturated PAH‐contaminated sites, anaerobic microorganisms are crucial for their consumption. Here, we report the metabolic pathway for anaerobic degradation of phenanthrene by a sulfate‐reducing enrichment culture (TRIP) obtained from a natural asphalt lake. The dominant organism of this culture belongs to the Desulfobacteraceae family of Deltaproteobacteria and genome‐resolved metagenomics led to the reconstruction of its genome along with a handful of genomes from lower abundance bacteria. Proteogenomic analyses confirmed metabolic capabilities for dissimilatory sulfate reduction and indicated the presence of the Embden‐Meyerhof‐Parnas pathway, a complete tricarboxylic acid cycle as well as a complete Wood‐Ljungdahl pathway. Genes encoding enzymes putatively involved in the degradation of phenanthrene were identified. This includes two gene clusters encoding a multisubunit carboxylase complex likely involved in the activation of phenanthrene, as well as genes encoding reductases potentially involved in subsequent ring dearomatization and reduction steps. The predicted metabolic pathways were corroborated by transcriptome and proteome analyses, and provide the first insights into the metabolic pathway responsible for the anaerobic degradation of three‐ringed PAHs.
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Affiliation(s)
- Ivana Kraiselburd
- Biofilm Centre, Aquatic Microbiology Department, Faculty of Chemistry, University Duisburg-Essen, Essen, Germany
| | - Thomas Brüls
- CEA, DRF, Institut Jacob, Genoscope, Evry, France.,CNRS-UMR8030, Université Paris-Saclay, Evry, France
| | - Geronimo Heilmann
- Centre of Medical Biotechnology, Chemical Biology Department, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Farnusch Kaschani
- Centre of Medical Biotechnology, Chemical Biology Department, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Markus Kaiser
- Centre of Medical Biotechnology, Chemical Biology Department, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Rainer U Meckenstock
- Biofilm Centre, Aquatic Microbiology Department, Faculty of Chemistry, University Duisburg-Essen, Essen, Germany
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46
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Himmelberg AM, Brüls T, Farmani Z, Weyrauch P, Barthel G, Schrader W, Meckenstock RU. Anaerobic degradation of phenanthrene by a sulfate-reducing enrichment culture. Environ Microbiol 2018; 20:3589-3600. [DOI: 10.1111/1462-2920.14335] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 06/21/2018] [Indexed: 11/28/2022]
Affiliation(s)
- Anne M. Himmelberg
- Institute of Groundwater Ecology; Helmholtz Zentrum München; Neuherberg Germany
| | - Thomas Brüls
- CEA, DRF, Institut Jacob, Genoscope; Evry France
- CNRS-UMR8030; Université Paris-Saclay; Evry France
| | - Zahra Farmani
- Biofilm Centre; University of Duisburg-Essen; Essen Germany
- Max-Planck-Institut für Kohlenforschung; Mülheim Germany
| | | | - Gabriele Barthel
- Institute of Groundwater Ecology; Helmholtz Zentrum München; Neuherberg Germany
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