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Chen SC, Musat F, Richnow HH, Krüger M. Microbial diversity and oil biodegradation potential of northern Barents Sea sediments. J Environ Sci (China) 2024; 146:283-297. [PMID: 38969457 DOI: 10.1016/j.jes.2023.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/29/2023] [Accepted: 12/07/2023] [Indexed: 07/07/2024]
Abstract
The Arctic, an essential ecosystem on Earth, is subject to pronounced anthropogenic pressures, most notable being the climate change and risks of crude oil pollution. As crucial elements of Arctic environments, benthic microbiomes are involved in climate-relevant biogeochemical cycles and hold the potential to remediate upcoming contamination. Yet, the Arctic benthic microbiomes are among the least explored biomes on the planet. Here we combined geochemical analyses, incubation experiments, and microbial community profiling to detail the biogeography and biodegradation potential of Arctic sedimentary microbiomes in the northern Barents Sea. The results revealed a predominance of bacterial and archaea phyla typically found in the deep marine biosphere, such as Chloroflexi, Atribacteria, and Bathyarcheaota. The topmost benthic communities were spatially structured by sedimentary organic carbon, lacking a clear distinction among geographic regions. With increasing sediment depth, the community structure exhibited stratigraphic variability that could be correlated to redox geochemistry of sediments. The benthic microbiomes harbored multiple taxa capable of oxidizing hydrocarbons using aerobic and anaerobic pathways. Incubation of surface sediments with crude oil led to proliferation of several genera from the so-called rare biosphere. These include Alkalimarinus and Halioglobus, previously unrecognized as hydrocarbon-degrading genera, both harboring the full genetic potential for aerobic alkane oxidation. These findings increase our understanding of the taxonomic inventory and functional potential of unstudied benthic microbiomes in the Arctic.
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Affiliation(s)
- Song-Can Chen
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany; Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Florin Musat
- Department of Biology, Section for Microbiology, Aarhus University, Aarhus, Denmark; Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeș-Bolyai University, Cluj-Napoca, Romania.
| | - Hans-Hermann Richnow
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Martin Krüger
- Federal Institute for Geosciences and Natural Resources (BGR), Stilleweg 2, 30655, Hannover, Germany
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2
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Skouroliakou D, Breton E, Christaki U. Phaeocystis globosa and diatom blooms promote distinct bacterial communities and associations in a coastal ecosystem. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13313. [PMID: 38988030 PMCID: PMC11236930 DOI: 10.1111/1758-2229.13313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Accepted: 06/26/2024] [Indexed: 07/12/2024]
Abstract
Phytoplankton and bacteria form the foundation of marine food webs. While most studies on phytoplankton bloom influence on bacteria dynamics focus on diatom-dominated blooms due to their global ecological significance, it is unclear if similar patterns extend to other species that compete with diatoms like Phaeocystis spp. This study aimed to contribute to the understanding of associations between phytoplankton and bacteria in a temperate ecosystem. For this, we studied the dynamics of phytoplankton and bacteria, combining 16S metabarcoding, microscopy, and flow cytometry over 4 years (282 samples). Phytoplankton and bacterial communities were studied throughout the year, particularly during contrasting phytoplankton blooms dominated by the Haptophyte Phaeocystis globosa or diatoms. We applied extended local similarity analysis (eLSA) to construct networks during blooming and non-blooming periods. Overall, the importance of seasonal and species-specific interactions between phytoplankton and bacteria is highlighted. In winter, mixed diatom communities were interconnected with bacteria, indicating a synergistic degradation of diverse phytoplankton-derived substrates. In spring, despite the intensity variations of P. globosa blooms, the composition of bacterial communities remained consistent over several years, suggesting establishing a stable-state environment for bacterial communities. Specific associations between monospecific diatom blooms and bacteria were evidenced in summer.
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Affiliation(s)
- Dimitra‐Ioli Skouroliakou
- UMR CNRS 8187 LOG, Université Littoral Côte d’Opale, Université de LilleWimereuxFrance
- Present address:
Laboratory of Protistology and Aquatic Ecology, Department of BiologyGhent UniversityGhentBelgium
| | - Elsa Breton
- UMR CNRS 8187 LOG, Université Littoral Côte d’Opale, Université de LilleWimereuxFrance
| | - Urania Christaki
- UMR CNRS 8187 LOG, Université Littoral Côte d’Opale, Université de LilleWimereuxFrance
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Hamamoto K, Mizuyama M, Nishijima M, Maeda A, Gibu K, Poliseno A, Iguchi A, Reimer JD. Diversity, composition and potential roles of sedimentary microbial communities in different coastal substrates around subtropical Okinawa Island, Japan. ENVIRONMENTAL MICROBIOME 2024; 19:54. [PMID: 39080706 PMCID: PMC11290285 DOI: 10.1186/s40793-024-00594-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 07/08/2024] [Indexed: 08/02/2024]
Abstract
BACKGROUND Marine benthic prokaryotic communities play crucial roles in material recycling within coastal environments, including coral reefs. Coastal sedimentary microbiomes are particularly important as potential reservoirs of symbiotic, beneficial, and pathogenic bacteria in coral reef environments, and therefore presumably play a core role in local ecosystem functioning. However, there is a lack of studies comparing different environments with multiple sites on the island scale, particularly studies focusing on prokaryotic communities, as previous investigations have focused mainly on a single site or on specific environmental conditions. In our study, we collected coastal sediments from seven sites around Okinawa Island, Japan, including three different benthic types; sandy bottoms, seagrass meadows, and hard substratum with living scleractinian corals. We then used metabarcoding to identify prokaryotic compositions and estimate enzymes encoded by genes to infer their functions. RESULTS The results showed that the three substrata had significantly different prokaryotic compositions. Seagrass meadow sites exhibited significantly higher prokaryotic alpha-diversity compared to sandy bottom sites. ANCOM analysis revealed that multiple bacterial orders were differentially abundant within each substratum. At coral reef sites, putative disease- and thermal stress-related opportunistic bacteria such as Rhodobacterales, Verrucomicrobiales, and Cytophagales were comparatively abundant, while seagrass meadow sites abundantly harbored Desulfobacterales, Steroidobacterales and Chromatiales, which are common bacterial orders in seagrass meadows. According to our gene-coded enzyme analyses the numbers of differentially abundant enzymes were highest in coral reef sites. Notably, superoxide dismutase, an important enzyme for anti-oxidative stress in coral tissue, was abundant at coral sites. Our results provide a list of prokaryotes to look into in each substrate, and further emphasize the importance of considering the microbiome, especially when focusing on environmental conservation. CONCLUSION Our findings prove that prokaryotic metabarcoding is capable of capturing compositional differences and the diversity of microbial communities in three different environments. Furthermore, several taxa were suggested to be differentially more abundant in specific environments, and gene-coded enzymic compositions also showed possible differences in ecological functions. Further study, in combination with field observations and temporal sampling, is key to achieving a better understanding of the interactions between the local microbiome and the surrounding benthic community.
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Affiliation(s)
- Kohei Hamamoto
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8567, Japan.
- Molecular Invertebrate Systematics and Ecology (MISE) Laboratory, Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Okinawa, 903-0213, Japan.
| | - Masaru Mizuyama
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8567, Japan
- Department of Health Informatics, Faculty of Human Health Sciences, Meio University, Nago, Okinawa, 905-8585, Japan
| | - Miyuki Nishijima
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8567, Japan
| | - Ayumi Maeda
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, 277-8564, Japan
| | - Kodai Gibu
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8567, Japan
| | - Angelo Poliseno
- Molecular Invertebrate Systematics and Ecology (MISE) Laboratory, Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Okinawa, 903-0213, Japan
| | - Akira Iguchi
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8567, Japan.
- Research Laboratory on Environmentally-Conscious Developments and Technologies [E-code], National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8567, Japan.
| | - James Davis Reimer
- Molecular Invertebrate Systematics and Ecology (MISE) Laboratory, Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Okinawa, 903-0213, Japan
- Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa, 903-0213, Japan
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Rasmussen TS, Mao X, Forster S, Larsen SB, Von Münchow A, Tranæs KD, Brunse A, Larsen F, Mejia JLC, Adamberg S, Hansen AK, Adamberg K, Hansen CHF, Nielsen DS. Overcoming donor variability and risks associated with fecal microbiota transplants through bacteriophage-mediated treatments. MICROBIOME 2024; 12:119. [PMID: 38951925 PMCID: PMC11218093 DOI: 10.1186/s40168-024-01820-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 04/19/2024] [Indexed: 07/03/2024]
Abstract
BACKGROUND Fecal microbiota transplantation (FMT) and fecal virome transplantation (FVT, sterile filtrated donor feces) have been effective in treating recurrent Clostridioides difficile infections, possibly through bacteriophage-mediated modulation of the gut microbiome. However, challenges like donor variability, costly screening, coupled with concerns over pathogen transfer (incl. eukaryotic viruses) with FMT or FVT hinder their wider clinical application in treating less acute diseases. METHODS To overcome these challenges, we developed methods to broaden FVT's clinical application while maintaining efficacy and increasing safety. Specifically, we employed the following approaches: (1) chemostat-fermentation to reproduce the bacteriophage FVT donor component and remove eukaryotic viruses (FVT-ChP), (2) solvent-detergent treatment to inactivate enveloped viruses (FVT-SDT), and (3) pyronin-Y treatment to inhibit RNA virus replication (FVT-PyT). We assessed the efficacy of these processed FVTs in a C. difficile infection mouse model and compared them with untreated FVT (FVT-UnT), FMT, and saline. RESULTS FVT-SDT, FVT-UnT, and FVT-ChP reduced the incidence of mice reaching the humane endpoint (0/8, 2/7, and 3/8, respectively) compared to FMT, FVT-PyT, and saline (5/8, 7/8, and 5/7, respectively) and significantly reduced the load of colonizing C. difficile cells and associated toxin A/B levels. There was a potential elimination of C. difficile colonization, with seven out of eight mice treated with FVT-SDT testing negative with qPCR. In contrast, all other treatments exhibited the continued presence of C. difficile. Moreover, the results were supported by changes in the gut microbiome profiles, cecal cytokine levels, and histopathological findings. Assessment of viral engraftment following FMT/FVT treatment and host-phage correlations analysis suggested that transfer of phages likely were an important contributing factor associated with treatment efficacy. CONCLUSIONS This proof-of-concept study shows that specific modifications of FVT hold promise in addressing challenges related to donor variability and infection risks. Two strategies lead to treatments significantly limiting C. difficile colonization in mice, with solvent/detergent treatment and chemostat propagation of donor phages emerging as promising approaches. Video Abstract.
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Affiliation(s)
- Torben Sølbeck Rasmussen
- Section of Food Microbiology, Gut Health, and Fermentation, Department of Food Science, University of Copenhagen, Rolighedsvej 26 4, 1958, Frederiksberg, Denmark.
| | - Xiaotian Mao
- Section of Food Microbiology, Gut Health, and Fermentation, Department of Food Science, University of Copenhagen, Rolighedsvej 26 4, 1958, Frederiksberg, Denmark
| | - Sarah Forster
- Section of Food Microbiology, Gut Health, and Fermentation, Department of Food Science, University of Copenhagen, Rolighedsvej 26 4, 1958, Frederiksberg, Denmark
| | - Sabina Birgitte Larsen
- Section of Food Microbiology, Gut Health, and Fermentation, Department of Food Science, University of Copenhagen, Rolighedsvej 26 4, 1958, Frederiksberg, Denmark
| | - Alexandra Von Münchow
- Section of Experimental Animal Models, Department, of Veterinary and Animal Sciences, University of Copenhagen, Ridebanevej 9 1, 1871, Frederiksberg, Denmark
| | - Kaare Dyekær Tranæs
- Section of Food Microbiology, Gut Health, and Fermentation, Department of Food Science, University of Copenhagen, Rolighedsvej 26 4, 1958, Frederiksberg, Denmark
| | - Anders Brunse
- Section of Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, University of Copenhagen, Dyrlægevej 68, 1870, Frederiksberg, Denmark
| | - Frej Larsen
- Section of Food Microbiology, Gut Health, and Fermentation, Department of Food Science, University of Copenhagen, Rolighedsvej 26 4, 1958, Frederiksberg, Denmark
| | - Josue Leonardo Castro Mejia
- Section of Food Microbiology, Gut Health, and Fermentation, Department of Food Science, University of Copenhagen, Rolighedsvej 26 4, 1958, Frederiksberg, Denmark
| | - Signe Adamberg
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618, Tallinn, Estonia
| | - Axel Kornerup Hansen
- Section of Experimental Animal Models, Department, of Veterinary and Animal Sciences, University of Copenhagen, Ridebanevej 9 1, 1871, Frederiksberg, Denmark
| | - Kaarel Adamberg
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618, Tallinn, Estonia
| | - Camilla Hartmann Friis Hansen
- Section of Experimental Animal Models, Department, of Veterinary and Animal Sciences, University of Copenhagen, Ridebanevej 9 1, 1871, Frederiksberg, Denmark
| | - Dennis Sandris Nielsen
- Section of Food Microbiology, Gut Health, and Fermentation, Department of Food Science, University of Copenhagen, Rolighedsvej 26 4, 1958, Frederiksberg, Denmark.
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Huang H, Zan S, Shao K, Chen H, Fan J. Spatial distribution characteristics and interaction effects of DOM and microbial communities in kelp cultivation areas. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 920:170511. [PMID: 38309352 DOI: 10.1016/j.scitotenv.2024.170511] [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: 08/30/2023] [Revised: 01/17/2024] [Accepted: 01/26/2024] [Indexed: 02/05/2024]
Abstract
The influence of macroalgae cultivation on aquaculture carbon sinks is significant, with microbial carbon (C) pumps contributing to a stable inert dissolved carbon pool in this context. Concurrently, dissolved organic matter (DOM) exchange at the marine sediment-water interface profoundly affects global ecosystem element cycling. However, the interactions between DOM and bacterial communities at the sediment-water interface in kelp cultivation areas, especially regarding microbial function prediction, have not been fully explored. This study analyzed the DOM characteristics, environmental factors, and bacterial community structure in the Tahewan kelp--Saccharina japonica cultivated area and compared them with those in non-cultivated areas. The results indicated significantly higher dissolved organic carbon (DOC) concentrations in the kelp culture area, particularly in surface seawater and overlying water. The dominant bacterial phyla in both regions included Pseudomonadota, Actinomycetota, and Bacteroidota in both regions, while Desulfobacterota was more prevalent in the sediment environment of the cultivated region. Parallel factor analysis (EEM-PARAFAC) was used to identify DOM components, among which component C2 (a microbial humic-like substance DOM) was highly resistant to microbial degradation. We infer that C2 has similar properties to recalcitrant dissolved organic matter (RDOM). Analysis of the predicted functional genes based on 16S rRNA gene data showed that methanol oxidation, methylotrophy, and methanotrophy were significant in the bottom seawater of the cultivation area. The carbon (C), nitrogen (N), and sulfur (S) cycle functional genes in the sediment environment of the kelp cultivation area were more active than those in other areas, especially in which sulfate reduction and denitrification were the two main processes. Furthermore, a DOM priming effect was identified in the cultivated sediment environment, where kelp-released labile dissolved organic matter (LDOM) stimulates rapid degradation of the original RDOM, potentially enhancing C sequestration.
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Affiliation(s)
- Huiling Huang
- College of Oceanography and Ecological Science, Shanghai Ocean University, Shanghai, China; State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, China
| | - Shuaijun Zan
- Groundwater Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Kuishuang Shao
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, China
| | - Hanjun Chen
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, China; College of Marine Technology and Environment, Dalian Ocean University, Dalian, China
| | - Jingfeng Fan
- College of Oceanography and Ecological Science, Shanghai Ocean University, Shanghai, China; State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, China; College of Marine Technology and Environment, Dalian Ocean University, Dalian, China.
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6
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Liu J, Li DW, He X, Liu R, Cheng H, Su C, Chen M, Wang Y, Zhao Z, Xu H, Cheng Z, Wang Z, Pedentchouk N, Lea-Smith DJ, Todd JD, Liu X, Zhao M, Zhang XH. A unique subseafloor microbiosphere in the Mariana Trench driven by episodic sedimentation. MARINE LIFE SCIENCE & TECHNOLOGY 2024; 6:168-181. [PMID: 38433963 PMCID: PMC10902237 DOI: 10.1007/s42995-023-00212-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 11/23/2023] [Indexed: 03/05/2024]
Abstract
Hadal trenches are characterized by enhanced and infrequent high-rate episodic sedimentation events that likely introduce not only labile organic carbon and key nutrients but also new microbes that significantly alter the subseafloor microbiosphere. Currently, the role of high-rate episodic sedimentation in controlling the composition of the hadal subseafloor microbiosphere is unknown. Here, analyses of carbon isotope composition in a ~ 750 cm long sediment core from the Challenger Deep revealed noncontinuous deposition, with anomalous 14C ages likely caused by seismically driven mass transport and the funneling effect of trench geomorphology. Microbial community composition and diverse enzyme activities in the upper ~ 27 cm differed from those at lower depths, probably due to sudden sediment deposition and differences in redox condition and organic matter availability. At lower depths, microbial population numbers, and composition remained relatively constant, except at some discrete depths with altered enzyme activity and microbial phyla abundance, possibly due to additional sudden sedimentation events of different magnitude. Evidence is provided of a unique role for high-rate episodic sedimentation events in controlling the subsurface microbiosphere in Earth's deepest ocean floor and highlight the need to perform thorough analysis over a large depth range to characterize hadal benthic populations. Such depositional processes are likely crucial in shaping deep-water geochemical environments and thereby the deep subseafloor biosphere. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-023-00212-y.
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Affiliation(s)
- Jiwen Liu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, 266237 China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| | - Da-Wei Li
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, 266237 China
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, 266100 China
| | - Xinxin He
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| | - Ronghua Liu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| | - Haojin Cheng
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| | - Chenglong Su
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, 266100 China
| | - Mengna Chen
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, 266100 China
| | - Yonghong Wang
- Key Lab of Submarine Geosciences and Prospecting Techniques, Ministry of Education/College of Marine Geosciences, Ocean University of China, Qingdao, 266100 China
| | - Zhongsheng Zhao
- Key Laboratory of Physical Oceanography, Ministry of Education/Research Vessel Centre, Ocean University of China, Qingdao, 266100 China
| | - Hanyue Xu
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, 266100 China
| | - Zhangyu Cheng
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, 266100 China
| | - Zicheng Wang
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, 266100 China
| | - Nikolai Pedentchouk
- School of Environmental Sciences, University of East Anglia, Norwich, NR4 7TJ UK
| | - David J. Lea-Smith
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ UK
| | - Jonathan D. Todd
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ UK
| | - Xiaoshou Liu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| | - Meixun Zhao
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, 266237 China
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, 266100 China
| | - Xiao-Hua Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, 266237 China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
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Layoun P, López-Pérez M, Haro-Moreno JM, Haber M, Thrash JC, Henson MW, Kavagutti VS, Ghai R, Salcher MM. Flexible genomic island conservation across freshwater and marine Methylophilaceae. THE ISME JOURNAL 2024; 18:wrad036. [PMID: 38365254 PMCID: PMC10872708 DOI: 10.1093/ismejo/wrad036] [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: 12/12/2023] [Revised: 12/15/2023] [Accepted: 12/20/2023] [Indexed: 02/18/2024]
Abstract
The evolutionary trajectory of Methylophilaceae includes habitat transitions from freshwater sediments to freshwater and marine pelagial that resulted in genome reduction (genome-streamlining) of the pelagic taxa. However, the extent of genetic similarities in the genomic structure and microdiversity of the two genome-streamlined pelagic lineages (freshwater "Ca. Methylopumilus" and the marine OM43 lineage) has so far never been compared. Here, we analyzed complete genomes of 91 "Ca. Methylopumilus" strains isolated from 14 lakes in Central Europe and 12 coastal marine OM43 strains. The two lineages showed a remarkable niche differentiation with clear species-specific differences in habitat preference and seasonal distribution. On the other hand, we observed a synteny preservation in their genomes by having similar locations and types of flexible genomic islands (fGIs). Three main fGIs were identified: a replacement fGI acting as phage defense, an additive fGI harboring metabolic and resistance-related functions, and a tycheposon containing nitrogen-, thiamine-, and heme-related functions. The fGIs differed in relative abundances in metagenomic datasets suggesting different levels of variability ranging from strain-specific to population-level adaptations. Moreover, variations in one gene seemed to be responsible for different growth at low substrate concentrations and a potential biogeographic separation within one species. Our study provides a first insight into genomic microdiversity of closely related taxa within the family Methylophilaceae and revealed remarkably similar dynamics involving mobile genetic elements and recombination between freshwater and marine family members.
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Affiliation(s)
- Paul Layoun
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre CAS, 37005 Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia, 37005 Ceske Budejovice, Czech Republic
| | - Mario López-Pérez
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, 03550 San Juan de Alicante, Spain
| | - Jose M Haro-Moreno
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, 03550 San Juan de Alicante, Spain
| | - Markus Haber
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre CAS, 37005 Ceske Budejovice, Czech Republic
| | - J Cameron Thrash
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Michael W Henson
- Department of Geophysical Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Vinicius Silva Kavagutti
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre CAS, 37005 Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia, 37005 Ceske Budejovice, Czech Republic
| | - Rohit Ghai
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre CAS, 37005 Ceske Budejovice, Czech Republic
| | - Michaela M Salcher
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre CAS, 37005 Ceske Budejovice, Czech Republic
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8
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Molina-Pardines C, Haro-Moreno JM, López-Pérez M. Phosphate-related genomic islands as drivers of environmental adaptation in the streamlined marine alphaproteobacterial HIMB59. mSystems 2023; 8:e0089823. [PMID: 38054740 PMCID: PMC10734472 DOI: 10.1128/msystems.00898-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 10/17/2023] [Indexed: 12/07/2023] Open
Abstract
IMPORTANCE These results shed light on the evolutionary strategies of microbes with streamlined genomes to adapt and survive in the oligotrophic conditions that dominate the surface waters of the global ocean. At the individual level, these microbes have been subjected to evolutionary constraints that have led to a more efficient use of nutrients, removing non-essential genes named as "streamlining theory." However, at the population level, they conserve a highly diverse gene pool in flexible genomic islands resulting in polyclonal populations on the same genomic background as an evolutionary response to environmental pressures. Localization of these islands at equivalent positions in the genome facilitates horizontal transfer between clonal lineages. This high level of environmental genomic heterogeneity could explain their cosmopolitan distribution. In the case of the order HIMB59 within the class Alphaproteobacteria, two factors exert evolutionary pressure and determine this intraspecific diversity: phages and the concentration of P in the environment.
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Affiliation(s)
- Carmen Molina-Pardines
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, San Juan, Alicante, Spain
| | - Jose M. Haro-Moreno
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, San Juan, Alicante, Spain
| | - Mario López-Pérez
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, San Juan, Alicante, Spain
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Gong S, Qin Y, Zheng S, Lu T, Yang X, Zeng M, Zhou H, Chen J, Huang W. The rapid start-up of CANON process through adding partial nitration sludge to ANAMMOX system. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 338:117821. [PMID: 37001425 DOI: 10.1016/j.jenvman.2023.117821] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 03/11/2023] [Accepted: 03/25/2023] [Indexed: 06/19/2023]
Abstract
This study aimed to start up the completely autotrophic nitrogen removal over nitrite (CANON) process after adding partial nitration (PN) sludge to the ANAMMOX reactor, so as to help the rapid start-up and stable operation of the CANON process in practical engineering applications. There were three steps in the research: cultivating the PN sludge, building a reliable ANAMMMOX system, and finally starting and running the CANON process. The PN sludge was successfully cultivated in less than 45 days with around 90% nitrite accumulation rate. The ANAMMOX reactor enriched a significant quantity of red granular sludge within 70 days, achieving the maximum nitrogen removal rate of 1.74 kg/(m3·d). Eventually, the CANON reactor was started up successfully, which achieved 95.08% of average ammonium removal efficiency and 84.51% of average total nitrogen removal efficiency in 60 days. The residual recalcitrant nitrite-oxidizing bacteria in the CANON process was successfully inhibited by intermittent aeration and 12 mg/L free ammonia in UASB reactor. Besides, Candidatus Kuenenia, Candidatus Brocadia and Nitrosomonas were the main functional microorganisms involved in the CANON process.
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Affiliation(s)
- Siyuan Gong
- School of Environment and Energy, South China University of Technology, Guangzhou Higher Education Mega Centre, Guangzhou, 510006, PR China
| | - Yujie Qin
- School of Environment and Energy, South China University of Technology, Guangzhou Higher Education Mega Centre, Guangzhou, 510006, PR China; The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, South China University of Technology, Guangzhou Higher Education Mega Centre, Guangzhou, 510006, PR China.
| | - Shaohong Zheng
- School of Environment and Energy, South China University of Technology, Guangzhou Higher Education Mega Centre, Guangzhou, 510006, PR China
| | - Tiansheng Lu
- School of Environment and Energy, South China University of Technology, Guangzhou Higher Education Mega Centre, Guangzhou, 510006, PR China
| | - Xiangjing Yang
- School of Environment and Energy, South China University of Technology, Guangzhou Higher Education Mega Centre, Guangzhou, 510006, PR China
| | - Ming Zeng
- School of Environment and Energy, South China University of Technology, Guangzhou Higher Education Mega Centre, Guangzhou, 510006, PR China
| | - Hongen Zhou
- School of Environment and Energy, South China University of Technology, Guangzhou Higher Education Mega Centre, Guangzhou, 510006, PR China
| | - Jiannv Chen
- School of Environment and Energy, South China University of Technology, Guangzhou Higher Education Mega Centre, Guangzhou, 510006, PR China
| | - Weichan Huang
- School of Environment and Energy, South China University of Technology, Guangzhou Higher Education Mega Centre, Guangzhou, 510006, PR China
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10
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Roda-Garcia JJ, Haro-Moreno JM, López-Pérez M. Evolutionary pathways for deep-sea adaptation in marine planktonic Actinobacteriota. Front Microbiol 2023; 14:1159270. [PMID: 37234526 PMCID: PMC10205998 DOI: 10.3389/fmicb.2023.1159270] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 04/24/2023] [Indexed: 05/28/2023] Open
Abstract
The deep ocean, one of the largest ecosystems on earth, is dominated by microorganisms that are keystones in the regulation of biogeochemical cycles. However, the evolutionary pathways underlying the specific adaptations required (e.g., high pressure and low temperature) by this unique niche remain understudied. Here, we analyzed the first representatives belonging to the order Acidimicrobiales, a group of marine planktonic Actinobacteriota, that specifically inhabits the aphotic zone of the oceanic water column (>200 m). Compared with their epipelagic counterparts, deep-sea representatives showed the same evolution in genome architecture with higher GC content, longer intergenic spaces as well as higher nitrogen (N-ARSC) and lower carbon (C-ARSC) content in encoded amino acid residue side chains consistent with the higher nitrogen concentration and lower carbon concentration in deep waters compared to the photic zone. Metagenomic recruitment showed distribution patterns that allowed the description of different ecogenomic units within the three deep water-associated genera defined by our phylogenomic analyses (UBA3125, S20-B6 and UBA9410). The entire genus UBA3125 was found exclusively associated with oxygen minimum zones linked to the acquisition of genes involved in denitrification. Genomospecies of genus S20-B6 recruited in samples from both mesopelagic (200-1,000 m) and bathypelagic (1000-4,000 m) zones, including polar regions. Diversity in the genus UBA9410 was higher, with genomospecies widely distributed in temperate zones, others in polar regions, and the only genomospecies associated with abyssal zones (>4,000 m). At the functional level, groups beyond the epipelagic zone have a more complex transcriptional regulation including in their genomes a unique WhiB paralog. In addition, they showed higher metabolic potential for organic carbon and carbohydrate degradation as well as the ability to accumulate glycogen as a source of carbon and energy. This could compensate for energy metabolism in the absence of rhodopsins, which is only present in genomes associated with the photic zone. The abundance in deep samples of cytochrome P450 monooxygenases associated with the genomes of this order suggests an important role in remineralization of recalcitrant compounds throughout the water column.
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11
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Roda-Garcia JJ, Haro-Moreno JM, Rodriguez-Valera F, Almagro-Moreno S, López-Pérez M. Single-amplified genomes reveal most streamlined free-living marine bacteria. Environ Microbiol 2023. [PMID: 36755376 DOI: 10.1111/1462-2920.16348] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 02/04/2023] [Indexed: 02/10/2023]
Abstract
Evolutionary adaptations of prokaryotes to the environment sometimes result in genome reduction. Our knowledge of this phenomenon among free-living bacteria remains scarce. We address the dynamics and limits of genome reduction by examining one of the most abundant bacteria in the ocean, the SAR86 clade. Despite its abundance, comparative genomics has been limited by the absence of pure cultures and the poor representation in metagenome-assembled genomes. We co-assembled multiple previously available single-amplified genomes to obtain the first complete genomes from members of the four families. All families showed a convergent evolutionary trajectory with characteristic features of streamlined genomes, most pronounced in the TMED112 family. This family has a genome size of ca. 1 Mb and only 1 bp as median intergenic distance, exceeding values found in other abundant microbes such as SAR11, OM43 and Prochlorococcus. This genomic simplification led to a reduction in the biosynthesis of essential molecules, DNA repair-related genes, and the ability to sense and respond to environmental factors, which could suggest an evolutionary dependence on other co-occurring microbes for survival (Black Queen hypothesis). Therefore, these reconstructed genomes within the SAR86 clade provide new insights into the limits of genome reduction in free-living marine bacteria.
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Affiliation(s)
- Juan J Roda-Garcia
- Evolutionary Genomics Group, Departamento Producción Vegetal y Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | - Jose M Haro-Moreno
- Evolutionary Genomics Group, Departamento Producción Vegetal y Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, Departamento Producción Vegetal y Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | - Salvador Almagro-Moreno
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida, USA.,National Center for Integrated Coastal Research, University of Central Florida, Orlando, Florida, USA
| | - Mario López-Pérez
- Evolutionary Genomics Group, Departamento Producción Vegetal y Microbiología, Universidad Miguel Hernández, Alicante, Spain
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12
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Le Moine Bauer S, Lu GS, Goulaouic S, Puzenat V, Schouw A, Barreyre T, Pawlowsky-Glahn V, Egozcue JJ, Martelat JE, Escartin J, Amend JP, Nomikou P, Vlasopoulos O, Polymenakou P, Jørgensen SL. Structure and metabolic potential of the prokaryotic communities from the hydrothermal system of Paleochori Bay, Milos, Greece. Front Microbiol 2023; 13:1060168. [PMID: 36687571 PMCID: PMC9852839 DOI: 10.3389/fmicb.2022.1060168] [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: 10/02/2022] [Accepted: 12/01/2022] [Indexed: 01/09/2023] Open
Abstract
Introduction Shallow hydrothermal systems share many characteristics with their deep-sea counterparts, but their accessibility facilitates their study. One of the most studied shallow hydrothermal vent fields lies at Paleochori Bay off the coast of Milos in the Aegean Sea (Greece). It has been studied through extensive mapping and its physical and chemical processes have been characterized over the past decades. However, a thorough description of the microbial communities inhabiting the bay is still missing. Methods We present the first in-depth characterization of the prokaryotic communities of Paleochori Bay by sampling eight different seafloor types that are distributed along the entire gradient of hydrothermal influence. We used deep sequencing of the 16S rRNA marker gene and complemented the analysis with qPCR quantification of the 16S rRNA gene and several functional genes to gain insights into the metabolic potential of the communities. Results We found that the microbiome of the bay is strongly influenced by the hydrothermal venting, with a succession of various groups dominating the sediments from the coldest to the warmest zones. Prokaryotic diversity and abundance decrease with increasing temperature, and thermophilic archaea overtake the community. Discussion Relevant geochemical cycles of the Bay are discussed. This study expands our limited understanding of subsurface microbial communities in acidic shallow-sea hydrothermal systems and the contribution of their microbial activity to biogeochemical cycling.
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Affiliation(s)
- Sven Le Moine Bauer
- Center for Deep Sea Research, Department of Earth Science, University of Bergen, Bergen, Norway,*Correspondence: Sven Le Moine Bauer,
| | - Guang-Sin Lu
- Cooperative Institute for Climate, Ocean and Ecosystem Studies, University of Washington, Seattle, WA, United States,NOAA Pacific Marine Environmental Laboratory, Seattle, WA, United States
| | - Steven Goulaouic
- Center for Deep Sea Research, Department of Earth Science, University of Bergen, Bergen, Norway
| | - Valentine Puzenat
- Institut de Physique du Globe de Paris, CNRS, Université Paris Cité, Paris, France
| | - Anders Schouw
- Center for Deep Sea Research, Department of Biology, University of Bergen, Bergen, Norway
| | - Thibaut Barreyre
- Center for Deep Sea Research, Department of Earth Science, University of Bergen, Bergen, Norway
| | - Vera Pawlowsky-Glahn
- Department of Computer Science, Applied Mathematics and Statistics, University of Girona, Girona, Spain
| | - Juan José Egozcue
- Department of Civil and Environmental Engineering, University Politécnica de Cataluña, Barcelona, Spain
| | - Jean-Emmanuel Martelat
- Université de Lyon, UCBL, ENSL, CNRS, Laboratoire de Géologie LGL-TPE, Villeurbanne, France
| | - Javier Escartin
- Laboratoire de Géologie (CNRS UMR8538), Ecole Normale Supérieure de Paris, PSL University, Paris, France
| | - Jan P. Amend
- Departments of Earth Sciences and Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Paraskevi Nomikou
- Faculty of Geology and Geoenvironment, National and Kapodistrian University of Athens, Athens, Greece
| | - Othonas Vlasopoulos
- Faculty of Geology and Geoenvironment, National and Kapodistrian University of Athens, Athens, Greece
| | - Paraskevi Polymenakou
- Institute of Marine Biology Biotechnology and Aquaculture, Hellenic Center for Marine Research, Heraklion, Greece
| | - Steffen Leth Jørgensen
- Center for Deep Sea Research, Department of Earth Science, University of Bergen, Bergen, Norway
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13
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Xu N, Wang W, Xu K, Xu Y, Ji D, Chen C, Xie C. Cultivation of different seaweed species and seasonal changes cause divergence of the microbial community in coastal seawaters. Front Microbiol 2022; 13:988743. [PMID: 36160253 PMCID: PMC9490310 DOI: 10.3389/fmicb.2022.988743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 08/17/2022] [Indexed: 12/02/2022] Open
Abstract
Although the effects of certain species of seaweed on the microbial community structure have long been a research focus in marine ecology, the response of the microbial community to seasons and different seaweed species is poorly understood. In the present study, a total of 39 seawater samples were collected during 3 months from three zones: Neoporphyra haitanensis cultivation zones (P), Gracilaria lemaneiformis-Saccharina japonica mixed cultivation zones (G), and control zones (C). These samples were then analyzed using 18S and 16S rRNA gene sequencing to ascertain the fungal and bacterial communities, respectively, along with the determination of environmental factors. Our results showed that increased dissolved oxygen (DO), decreased inorganic nutrients, and released dissolved organic matter (DOM) in seaweed cultivation zone predominantly altered the variability of eukaryotic and prokaryotic microbial communities. Certain microbial groups such as Aurantivirga, Pseudomonas, and Woeseia were stimulated and enriched in response to seaweed cultivation, and the enriched microorganisms varied across seaweed cultivation zones due to differences in the composition of released DOM. In addition, seasonal changes in salinity and temperature were strongly correlated with microbial community composition and structure. Our study provides new insights into the interactions between seaweed and microbial communities.
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Affiliation(s)
- Ningning Xu
- Fisheries College, Jimei University, Xiamen, China
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Xiamen, China
- Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen, China
| | - Wenlei Wang
- Fisheries College, Jimei University, Xiamen, China
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Xiamen, China
- Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen, China
| | - Kai Xu
- Fisheries College, Jimei University, Xiamen, China
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Xiamen, China
- Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen, China
| | - Yan Xu
- Fisheries College, Jimei University, Xiamen, China
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Xiamen, China
- Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen, China
| | - Dehua Ji
- Fisheries College, Jimei University, Xiamen, China
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Xiamen, China
- Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen, China
| | - Changsheng Chen
- Fisheries College, Jimei University, Xiamen, China
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Xiamen, China
- Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen, China
| | - Chaotian Xie
- Fisheries College, Jimei University, Xiamen, China
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Xiamen, China
- Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen, China
- *Correspondence: Chaotian Xie,
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14
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Phylogenomics of SAR116 Clade Reveals Two Subclades with Different Evolutionary Trajectories and an Important Role in the Ocean Sulfur Cycle. mSystems 2021; 6:e0094421. [PMID: 34609172 PMCID: PMC8547437 DOI: 10.1128/msystems.00944-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The SAR116 clade within the class Alphaproteobacteria represents one of the most abundant groups of heterotrophic bacteria inhabiting the surface of the ocean. The small number of cultured representatives of SAR116 (only two to date) is a major bottleneck that has prevented an in-depth study at the genomic level to understand the relationship between genome diversity and its role in the marine environment. In this study, we use all publicly available genomes to provide a genomic overview of the phylogeny, metabolism, and biogeography within the SAR116 clade. This increased genomic diversity has led to the discovery of two subclades that, despite coexisting in the same environment, display different properties in their genomic makeup. One represents a novel subclade for which no pure cultures have been isolated and is composed mainly of single-amplified genomes (SAGs). Genomes within this subclade showed convergent evolutionary trajectories with more streamlined features, such as low GC content (ca. 30%), short intergenic spacers (<22 bp), and strong purifying selection (low ratio of nonsynonymous to synonymous polymorphisms [dN/dS]). Besides, they were more abundant in metagenomic databases recruiting at the deep chlorophyll maximum. Less abundant and restricted to the upper photic layers of the global ocean, the other subclade of SAR116, enriched in metagenome-assembled genomes (MAGs), included the only two pure cultures. Genomic analysis suggested that both clades have a significant role in the sulfur cycle with differences in the way both clades can metabolize dimethylsulfoniopropionate (DMSP). IMPORTANCE The SAR116 clade of Alphaproteobacteria is a ubiquitous group of heterotrophic bacteria inhabiting the surface of the ocean, but the information about their ecology and population genomic diversity is scarce due to the difficulty of getting pure culture isolates. The combination of single-cell genomics and metagenomics has become an alternative approach to study these kinds of microbes. Our results expand the understanding of the genomic diversity, distribution, and lifestyles within this clade and provide evidence of different evolutionary trajectories in the genomic makeup of the two subclades that could serve to illustrate how evolutionary pressure can drive different adaptations to the same environment. Therefore, the SAR116 clade represents an ideal model organism for the study of the evolutionary streamlining of genomes in microbes that have relatively close relatedness to each other.
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15
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Haro-Moreno JM, López-Pérez M, Rodriguez-Valera F. Enhanced Recovery of Microbial Genes and Genomes From a Marine Water Column Using Long-Read Metagenomics. Front Microbiol 2021; 12:708782. [PMID: 34512586 PMCID: PMC8430335 DOI: 10.3389/fmicb.2021.708782] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 07/30/2021] [Indexed: 12/12/2022] Open
Abstract
Third-generation sequencing has penetrated little in metagenomics due to the high error rate and dependence for assembly on short-read designed bioinformatics. However, second-generation sequencing metagenomics (mostly Illumina) suffers from limitations, particularly in the assembly of microbes with high microdiversity and retrieval of the flexible (adaptive) fraction of prokaryotic genomes. Here, we have used a third-generation technique to study the metagenome of a well-known marine sample from the mixed epipelagic water column of the winter Mediterranean. We have compared PacBio Sequel II with the classical approach using Illumina Nextseq short reads followed by assembly to study the metagenome. Long reads allow for efficient direct retrieval of complete genes avoiding the bias of the assembly step. Besides, the application of long reads on metagenomic assembly allows for the reconstruction of much more complete metagenome-assembled genomes (MAGs), particularly from microbes with high microdiversity such as Pelagibacterales. The flexible genome of reconstructed MAGs was much more complete containing many adaptive genes (some with biotechnological potential). PacBio Sequel II CCS appears particularly suitable for cellular metagenomics due to its low error rate. For most applications of metagenomics, from community structure analysis to ecosystem functioning, long reads should be applied whenever possible. Specifically, for in silico screening of biotechnologically useful genes, or population genomics, long-read metagenomics appears presently as a very fruitful approach and can be analyzed from raw reads before a computationally demanding (and potentially artifactual) assembly step.
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Affiliation(s)
- Jose M. Haro-Moreno
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | - Mario López-Pérez
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Alicante, Spain
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
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16
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Huang Z, Mo S, Yan L, Wei X, Huang Y, Zhang L, Zhang S, Liu J, Xiao Q, Lin H, Guo Y. A Simple Culture Method Enhances the Recovery of Culturable Actinobacteria From Coastal Sediments. Front Microbiol 2021; 12:675048. [PMID: 34194410 PMCID: PMC8236954 DOI: 10.3389/fmicb.2021.675048] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 05/12/2021] [Indexed: 01/19/2023] Open
Abstract
Molecular methods revealed that the majority of microbes in natural environments remains uncultivated. To fully understand the physiological and metabolic characteristics of microbes, however, culturing is still critical for microbial studies. Here, we used bacterial community analysis and four culture media, namely, traditional marine broth 2216 (MB), water extracted matter (WEM), methanol extracted matter (MEM), and starch casein agar (SCA), to investigate the diversity of cultivated bacteria in coastal sediments. A total of 1,036 isolates were obtained in pure culture, and they were classified into five groups, namely, Alphaproteobacteria (52.51%), Gammaproteobacteria (23.26%), Actinobacteria (13.32%), Firmicutes, and Bacteroidetes. Compared to other three media, WEM recovered a high diversity of actinobacteria (42 of 63 genotypes), with Micromonospora and Streptomyces as the most cultivated genera. Amplicon sequencing of the bacterial 16S ribosomal RNA (rRNA) gene V3-V4 fragment revealed eight dominant groups, Alphaproteobacteria (12.81%), Gammaproteobacteria (20.07%), Deltaproteobacteria (12.95%), Chloroflexi (13.09%), Bacteroidetes (8.28%), Actinobacteria (7.34%), Cyanobacteria (6.20%), and Acidobacteria (5.71%). The dominant members affiliated to Actinobacteria belonged to "Candidatus Actinomarinales," "Candidatus Microtrichales," and Nitriliruptorales. The cultivated actinobacteria accounted for a small proportion (<5%) compared to the actinobacterial community, which supported that the majority of actinobacteria are still waiting for cultivation. Our study concluded that WEM could be a useful and simple culture medium that enhanced the recovery of culturable actinobacteria from coastal sediments.
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Affiliation(s)
- Zhaobin Huang
- College of Oceanology and Food Science, Quanzhou Normal University, Quanzhou, China
- Fujian Province Key Laboratory for the Development of Bioactive Material From Marine Algae, Quanzhou, China
| | - Shiqing Mo
- College of Oceanology and Food Science, Quanzhou Normal University, Quanzhou, China
| | - Lifei Yan
- College of Oceanology and Food Science, Quanzhou Normal University, Quanzhou, China
| | - Xiaomei Wei
- College of Oceanology and Food Science, Quanzhou Normal University, Quanzhou, China
| | - Yuanyuan Huang
- College of Oceanology and Food Science, Quanzhou Normal University, Quanzhou, China
| | - Lizhen Zhang
- College of Oceanology and Food Science, Quanzhou Normal University, Quanzhou, China
| | - Shuhui Zhang
- College of Oceanology and Food Science, Quanzhou Normal University, Quanzhou, China
| | - Jianzong Liu
- College of Oceanology and Food Science, Quanzhou Normal University, Quanzhou, China
| | - Qingqing Xiao
- College of Oceanology and Food Science, Quanzhou Normal University, Quanzhou, China
| | - Hong Lin
- College of Oceanology and Food Science, Quanzhou Normal University, Quanzhou, China
| | - Yu Guo
- College of Oceanology and Food Science, Quanzhou Normal University, Quanzhou, China
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