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Zhang W, Geng J, Sun M, Jiang C, Lin H, Chen H, Yang Y. Distinct species turnover patterns shaped the richness of antibiotic resistance genes on eight different microplastic polymers. ENVIRONMENTAL RESEARCH 2024; 259:119562. [PMID: 38971360 DOI: 10.1016/j.envres.2024.119562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 05/31/2024] [Accepted: 07/03/2024] [Indexed: 07/08/2024]
Abstract
Elucidating the formation mechanism of plastisphere antibiotic resistance genes (ARGs) on different polymers is necessary to understand the ecological risks of plastisphere ARGs. Here, we explored the turnover and assembly mechanism of plastisphere ARGs on 8 different microplastic polymers (4 biodegradable (bMPs) and 4 non-biodegradable microplastics (nMPs)) by metagenomic sequencing. Our study revealed the presence of 479 ARGs with abundance ranging from 41.37 to 58.17 copies/16S rRNA gene in all plastispheres. These ARGs were predominantly multidrug resistance genes. The richness of plastisphere ARGs on different polymers had a significant correlation with the contribution of species turnover to plastisphere ARGs β diversity. Furthermore, polymer type was the most critical factor affecting the composition of plastisphere ARGs. More opportunistic pathogens carrying diverse ARGs on BMPs (PBAT, PBS, and PHA) with higher horizontal gene transfer potential may further magnify the ecological risks and human health threats. For example, the opportunistic pathogens Riemerella anatipestifer, Vibrio campbellii, and Vibrio cholerae are closely related to human production and life, which were the important potential hosts of many plastisphere ARGs and mobile genetic elements on BMPs. Thus, we emphasize the urgency of developing the formation mechanism of plastisphere ARGs and the necessity of controlling BMPs and ARG pollution, especially BMPs, with ever-increasing usage in daily life.
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Affiliation(s)
- Weihong Zhang
- Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Key Laboratory of Lake and Watershed Science for Water Security, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, The Chinese Academy of Sciences & Hubei Province, Wuhan, 430074, China
| | - Jun Geng
- Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Key Laboratory of Lake and Watershed Science for Water Security, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, The Chinese Academy of Sciences & Hubei Province, Wuhan, 430074, China
| | - Mengge Sun
- Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China; School of Ocean Sciences, China University of Geosciences, Beijing, 100083, China
| | - Chunxia Jiang
- Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China; Key Laboratory of Lake and Watershed Science for Water Security, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, The Chinese Academy of Sciences & Hubei Province, Wuhan, 430074, China
| | - Hui Lin
- Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Environment, Resource, Soil and Fertilizers, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
| | - Haiyang Chen
- College of Water Sciences, Beijing Normal University, Beijing, 100875, China
| | - Yuyi Yang
- Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Key Laboratory of Lake and Watershed Science for Water Security, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, The Chinese Academy of Sciences & Hubei Province, Wuhan, 430074, China.
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2
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Guider JT, Yoshimura KM, Block KR, Biddle JF, Shah Walter SR. Archaeal blooms and busts in an estuarine time series. Environ Microbiol 2024; 26:e16584. [PMID: 38372423 DOI: 10.1111/1462-2920.16584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 01/22/2024] [Indexed: 02/20/2024]
Abstract
Coastal bays, such as Delaware Bay, are highly productive, ecologically important transitions between rivers and the coastal ocean. They offer opportunities to investigate archaeal assemblages across seasons, with the exchange of water masses that occurs with tidal cycles, and in the context of variable organic matter quality. For a year-long estuarine, size-fractionated time series, we used amplicon sequencing, chemical measurements, and qPCR to follow archaeal groups through the seasons. We detected seasonally high abundances of Marine Group II archaea in summer months which correlate with indicators of phytoplankton production, although not phytoplankton biomass. Although previous studies have reported associations between Marine Group II archaea and particles, here they are almost entirely found in very small particles (0.22-0.7 μm), suggesting they are free-living cells. Populations of Nitrososphaeria did not vary with particle size or environmental conditions. Methanogens were significant fractions of archaeal sequences in large particles at low tide during winter months. Contrary to expectations, Nanoarchaeia were found predominantly in the free-living fraction despite the previous observation that they require an association with hosts. These results underscore the utility of time series studies in shallow, tidally mixed estuarine environments that capture variable conditions for understanding the ecology and biogeochemistry of planktic archaea.
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Affiliation(s)
- Justin T Guider
- School of Marine Science and Policy, University of Delaware, Lewes, Delaware, USA
| | - Kristin M Yoshimura
- Department of Biology, James Madison University, Harrisonburg, Virginia, USA
| | - Kaleigh R Block
- School of Marine Science and Policy, University of Delaware, Lewes, Delaware, USA
| | - Jennifer F Biddle
- School of Marine Science and Policy, University of Delaware, Lewes, Delaware, USA
| | - Sunita R Shah Walter
- School of Marine Science and Policy, University of Delaware, Lewes, Delaware, USA
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Zhang W, Bhagwat G, Palanisami T, Liang S, Wan W, Yang Y. Lacustrine plastisphere: Distinct succession and assembly processes of prokaryotic and eukaryotic communities and role of site, time, and polymer types. WATER RESEARCH 2024; 248:120875. [PMID: 37992636 DOI: 10.1016/j.watres.2023.120875] [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: 08/08/2023] [Revised: 11/02/2023] [Accepted: 11/14/2023] [Indexed: 11/24/2023]
Abstract
Microplastics as a carrier can promote microbial diffusion, potentially influencing the ecological functions of microbial communities in aquatic environments. However, our understanding of the assembly mechanism of microbial communities on different microplastic polymers in freshwater lakes during succession is still insufficient, especially for the eukaryotes. Here, the colonization time, site, and polymer types of microplastics were comprehensively considered to investigate the composition and assembly of prokaryotic and eukaryotic communities and their driving factors during the lacustrine plastisphere formation. Results showed that the particle-associated microorganisms in water were the main source of the plastisphere prokaryotes, while the free-living microorganisms in water mainly accounted for the plastisphere eukaryotes. The response of prokaryotic communities to different microplastic polymers was stronger than eukaryotic communities. The assembly of plastisphere prokaryotic communities was dominated by homogenizing processes (mainly homogenous selection), while the assembly of eukaryotic communities was dominated by differentiating processes (mainly dispersal limitation). Colonization time was an important factor affecting the composition of prokaryotic and eukaryotic communities during the formation of the plastisphere. The Chao1 richness of prokaryotic communities in the plastisphere increased with the increase of colonization time, whereas the opposite was true in eukaryotic communities. This differential response of species diversity and composition of prokaryotic and eukaryotic communities in the plastisphere during dynamic succession could lead to their distinct assembly processes. Overall, the results suggest that distinct assembly of microbial communities in the plastisphere may depend more on specific microbial sub-communities and colonization time than polymer types and colonization site.
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Affiliation(s)
- Weihong Zhang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, the Chinese Academy of Sciences & Hubei Province, Wuhan 430074, China
| | - Geetika Bhagwat
- Environmental Plastic and Innovation Cluster, Global Innovation Centre for Advanced Nanomaterials, The University of Newcastle, 2308, NSW, Australia
| | - Thava Palanisami
- Environmental Plastic and Innovation Cluster, Global Innovation Centre for Advanced Nanomaterials, The University of Newcastle, 2308, NSW, Australia
| | - Shuxin Liang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China; School of Ecology and Environment, Tibet University, Lhasa 850000, China
| | - Wenjie Wan
- University of Chinese Academy of Sciences, Beijing, 100049, China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, the Chinese Academy of Sciences & Hubei Province, Wuhan 430074, China
| | - Yuyi Yang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, the Chinese Academy of Sciences & Hubei Province, Wuhan 430074, China.
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4
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Sanz-Sáez I, Sánchez P, Salazar G, Sunagawa S, de Vargas C, Bowler C, Sullivan MB, Wincker P, Karsenti E, Pedrós-Alió C, Agustí S, Gojobori T, Duarte CM, Gasol JM, Sánchez O, Acinas SG. Top abundant deep ocean heterotrophic bacteria can be retrieved by cultivation. ISME COMMUNICATIONS 2023; 3:92. [PMID: 37660234 PMCID: PMC10475052 DOI: 10.1038/s43705-023-00290-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 07/25/2023] [Accepted: 08/01/2023] [Indexed: 09/04/2023]
Abstract
Traditional culture techniques usually retrieve a small fraction of the marine microbial diversity, which mainly belong to the so-called rare biosphere. However, this paradigm has not been fully tested at a broad scale, especially in the deep ocean. Here, we examined the fraction of heterotrophic bacterial communities in photic and deep ocean layers that could be recovered by culture-dependent techniques at a large scale. We compared 16S rRNA gene sequences from a collection of 2003 cultured heterotrophic marine bacteria with global 16S rRNA metabarcoding datasets (16S TAGs) covering surface, mesopelagic and bathypelagic ocean samples that included 16 of the 23 samples used for isolation. These global datasets represent 60 322 unique 16S amplicon sequence variants (ASVs). Our results reveal a significantly higher proportion of isolates identical to ASVs in deeper ocean layers reaching up to 28% of the 16S TAGs of the bathypelagic microbial communities, which included the isolation of 3 of the top 10 most abundant 16S ASVs in the global bathypelagic ocean, related to the genera Sulfitobacter, Halomonas and Erythrobacter. These isolates contributed differently to the prokaryotic communities across different plankton size fractions, recruiting between 38% in the free-living fraction (0.2-0.8 µm) and up to 45% in the largest particles (20-200 µm) in the bathypelagic ocean. Our findings support the hypothesis that sinking particles in the bathypelagic act as resource-rich habitats, suitable for the growth of heterotrophic bacteria with a copiotroph lifestyle that can be cultured, and that these cultivable bacteria can also thrive as free-living bacteria.
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Affiliation(s)
- Isabel Sanz-Sáez
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, 08003, Barcelona, Spain.
| | - Pablo Sánchez
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, 08003, Barcelona, Spain
| | - Guillem Salazar
- Department of Biology, Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, CH-8093, Zurich, Switzerland
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, CH-8093, Zurich, Switzerland
| | - Colomban de Vargas
- Sorbonne University, CNRS, Station Biologique de Roscoff, UMR7144, ECOMAP, Roscoff, France
| | - Chris Bowler
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France
| | - Matthew B Sullivan
- Departments of Microbiology and Civil, Environmental and Geodetic Engineering; The Ohio State University, Columbus, OH, 43210, USA
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Énergie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, 91000, Evry, France
| | - Eric Karsenti
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016, Paris, France
- Directors' Research European Molecular Biology Laboratory, 69117, Heidelberg, Germany
| | - Carlos Pedrós-Alió
- Department of Systems Biology, Centro Nacional de Biotecnología (CNB), CSIC, 28049, Madrid, Spain
| | - Susana Agustí
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Takashi Gojobori
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Carlos M Duarte
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Josep M Gasol
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, 08003, Barcelona, Spain
| | - Olga Sánchez
- Departament de Genètica i Microbiologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.
| | - Silvia G Acinas
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, 08003, Barcelona, Spain.
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5
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Shan X, Szabo RE, Cordero OX. Mutation-induced infections of phage-plasmids. Nat Commun 2023; 14:2049. [PMID: 37041135 PMCID: PMC10090143 DOI: 10.1038/s41467-023-37512-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 03/17/2023] [Indexed: 04/13/2023] Open
Abstract
Phage-plasmids are extra-chromosomal elements that act both as plasmids and as phages, whose eco-evolutionary dynamics remain poorly constrained. Here, we show that segregational drift and loss-of-function mutations play key roles in the infection dynamics of a cosmopolitan phage-plasmid, allowing it to create continuous productive infections in a population of marine Roseobacter. Recurrent loss-of-function mutations in the phage repressor that controls prophage induction leads to constitutively lytic phage-plasmids that spread rapidly throughout the population. The entire phage-plasmid genome is packaged into virions, which were horizontally transferred by re-infecting lysogenized cells, leading to an increase in phage-plasmid copy number and to heterozygosity in a phage repressor locus in re-infected cells. However, the uneven distribution of phage-plasmids after cell division (i.e., segregational drift) leads to the production of offspring carrying only the constitutively lytic phage-plasmid, thus restarting the lysis-reinfection-segregation life cycle. Mathematical models and experiments show that these dynamics lead to a continuous productive infection of the bacterial population, in which lytic and lysogenic phage-plasmids coexist. Furthermore, analyses of marine bacterial genome sequences indicate that the plasmid backbone here can carry different phages and disseminates trans-continentally. Our study highlights how the interplay between phage infection and plasmid genetics provides a unique eco-evolutionary strategy for phage-plasmids.
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Affiliation(s)
- Xiaoyu Shan
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Rachel E Szabo
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Microbiology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Otto X Cordero
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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6
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Determination and quantification of microbial communities and antimicrobial resistance on food through host DNA-depleted metagenomics. Food Microbiol 2023; 110:104162. [DOI: 10.1016/j.fm.2022.104162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 09/28/2022] [Accepted: 10/09/2022] [Indexed: 11/05/2022]
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7
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Frequent Occurrence and Metabolic Versatility of Marinifilaceae Bacteria as Key Players in Organic Matter Mineralization in Global Deep Seas. mSystems 2022; 7:e0086422. [PMID: 36342154 PMCID: PMC9765461 DOI: 10.1128/msystems.00864-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Transfer of animal and plant detritus of both terrestrial and marine origins to the deep sea occurs on a global scale. Microorganisms play an important role in mineralizing them therein, but these are yet to be identified in situ. To observe key bacteria involved, we conducted long-term in situ incubation and found that members of the family Marinifilaceae (MF) occurred as some of the most predominant bacteria thriving on the new inputs of plant and animal biomasses in the deep sea in both marginal and oceanic areas. This taxon is diverse and ubiquitous in marine environments. A total of 11 MAGs belonging to MF were retrieved from metagenomic data and diverged into four subgroups in the phylogenomic tree. Based on metagenomic and metatranscriptomic analyses, we described the metabolic features and in situ metabolizing activities of different subgroups. The MF-2 subgroup, which dominates plant detritus-enriched cultures, specializes in polysaccharide degradation and lignin oxidation and has high transcriptional activities of related genes in situ. Intriguingly, members of this subgroup encode a nitrogen fixation pathway to compensate for the shortage of nitrogen sources inside the plant detritus. In contrast, other subgroups dominating the animal tissue-supported microbiomes are distinguished from MF-2 with regard to carbon and nitrogen metabolism and exhibit high transcriptional activity for proteolysis in situ. Despite these metabolic divergences of MF lineages, they show high in situ transcriptional activities for organic fermentation and anaerobic respiration (reductions of metal and/or dimethyl sulfoxide). These results highlight the role of previously unrecognized Marinifilaceae bacteria in organic matter mineralization in marine environments by coupling carbon and nitrogen cycling with metal and sulfur. IMPORTANCE Microbial mineralization of organic matter has a significant impact on the global biogeochemical cycle. This report confirms the role of Marinifilaceae in organic degradation in the oceans, with a contribution to ocean carbon cycling that has previously been underestimated. It was the dominant taxon thriving on plant and animal biomasses in our in situ incubator, as well as in whale falls and wood falls. At least 9 subgroups were revealed, and they were widely distributed in oceans globally but predominant in organic-matter-rich environments, with an average relative abundance of 8.3%. Different subgroups display a preference for the degradation of different macromolecules (polysaccharides, lignin, and protein) and adapt to their environments via special metabolic mechanisms.
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8
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Kukkar D, Sharma PK, Kim KH. Recent advances in metagenomic analysis of different ecological niches for enhanced biodegradation of recalcitrant lignocellulosic biomass. ENVIRONMENTAL RESEARCH 2022; 215:114369. [PMID: 36165858 DOI: 10.1016/j.envres.2022.114369] [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: 08/12/2022] [Revised: 09/06/2022] [Accepted: 09/15/2022] [Indexed: 06/16/2023]
Abstract
Lignocellulose wastes stemming from agricultural residues can offer an excellent opportunity as alternative energy solutions in addition to fossil fuels. Besides, the unrestrained burning of agricultural residues can lead to the destruction of the soil microflora and associated soil sterilization. However, the difficulties associated with the biodegradation of lignocellulose biomasses remain as a formidable challenge for their sustainable management. In this respect, metagenomics can be used as an effective option to resolve such dilemma because of its potential as the next generation sequencing technology and bioinformatics tools to harness novel microbial consortia from diverse environments (e.g., soil, alpine forests, and hypersaline/acidic/hot sulfur springs). In light of the challenges associated with the bulk-scale biodegradation of lignocellulose-rich agricultural residues, this review is organized to help delineate the fundamental aspects of metagenomics towards the assessment of the microbial consortia and novel molecules (such as biocatalysts) which are otherwise unidentifiable by conventional laboratory culturing techniques. The discussion is extended further to highlight the recent advancements (e.g., from 2011 to 2022) in metagenomic approaches for the isolation and purification of lignocellulolytic microbes from different ecosystems along with the technical challenges and prospects associated with their wide implementation and scale-up. This review should thus be one of the first comprehensive reports on the metagenomics-based analysis of different environmental samples for the isolation and purification of lignocellulose degrading enzymes.
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Affiliation(s)
- Deepak Kukkar
- Department of Biotechnology, Chandigarh University, Gharuan, Mohali - 140413, Punjab, India; University Centre for Research and Development, Chandigarh University, Gharuan, Mohali - 140413, Punjab, India.
| | | | - Ki-Hyun Kim
- Department of Civil and Environmental Engineering, Hanyang University, Seongdong-gu, Wangsimni-ro, Seoul - 04763, South Korea.
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9
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Shi J, Zuo Y, Qu W, Liu X, Fan Y, Cao P, Wang J. Stochastic processes shape the aggregation of free-living and particle-attached bacterial communities in the Yangtze River Estuary, China. J Basic Microbiol 2022; 62:1514-1525. [PMID: 35835725 DOI: 10.1002/jobm.202100666] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 06/16/2022] [Accepted: 06/26/2022] [Indexed: 11/05/2022]
Abstract
An estuary plays an important role in material and energy exchange between the land and sea, where complex physical, chemical, and biological processes occur. Here, we investigated the assembly processes of free-living (FL) and particle-associated (PA) bacterial communities in two seawater layers at five stations in the Yangtze River Estuary (YRE) by using 16S rRNA sequencing methods. The results indicated that Proteobacteria was the most abundant phylum in the YRE. The α-diversity of PA community was significantly higher than FL community, and analysis of similarity showed significantly different (Global R = 0.2809, p < 0.005). RDA revealed that phosphate (PO4 3- ) was significantly correlated with PA bacterial community abundance (p < 0.05). An ecological null model showed that both PA and FL bacterial communities were mainly influenced by stochastic processes (PA: 100%, FL: 70%), which PA attached to nutrient particles and are less affected by environmental filtration. Dispersal limitation (50%) was the main assembly process of the PA community, while homogeneous selection (30%) and drift (30%) were important processes in the FL community assembly. The available substrate for colonization limits the transformation from FL to PA bacteria. This study would improve our understanding of FL and PA bacterial community structure and factors affecting assembly process in estuarine environments.
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Affiliation(s)
- Jing Shi
- Marine Microorganism Ecological & Application Lab, Zhejiang Ocean University, Zhejiang, China
| | - Yaqiang Zuo
- Marine Microorganism Ecological & Application Lab, Zhejiang Ocean University, Zhejiang, China
| | - Wu Qu
- Marine Microorganism Ecological & Application Lab, Zhejiang Ocean University, Zhejiang, China
| | - Xuezhu Liu
- Marine Microorganism Ecological & Application Lab, Zhejiang Ocean University, Zhejiang, China
| | - Yingping Fan
- Marine Microorganism Ecological & Application Lab, Zhejiang Ocean University, Zhejiang, China
| | - Pinglin Cao
- Marine Microorganism Ecological & Application Lab, Zhejiang Ocean University, Zhejiang, China
| | - Jianxin Wang
- Marine Microorganism Ecological & Application Lab, Zhejiang Ocean University, Zhejiang, China
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10
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Luo E, Leu AO, Eppley JM, Karl DM, DeLong EF. Diversity and origins of bacterial and archaeal viruses on sinking particles reaching the abyssal ocean. THE ISME JOURNAL 2022; 16:1627-1635. [PMID: 35236926 PMCID: PMC9122931 DOI: 10.1038/s41396-022-01202-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 01/09/2022] [Accepted: 01/25/2022] [Indexed: 11/15/2022]
Abstract
Sinking particles and particle-associated microbes influence global biogeochemistry through particulate matter export from the surface to the deep ocean. Despite ongoing studies of particle-associated microbes, viruses in these habitats remain largely unexplored. Whether, where, and which viruses might contribute to particle production and export remain open to investigation. In this study, we analyzed 857 virus population genomes associated with sinking particles collected over three years in sediment traps moored at 4000 m in the North Pacific Subtropical Gyre. Particle-associated viruses here were linked to cellular hosts through matches to bacterial and archaeal metagenome-assembled genome (MAG)-encoded prophages or CRISPR spacers, identifying novel viruses infecting presumptive deep-sea bacteria such as Colwellia, Moritella, and Shewanella. We also identified lytic viruses whose abundances correlated with particulate carbon flux and/or were exported from the photic to abyssal ocean, including cyanophages. Our data are consistent with some of the predicted outcomes of the viral shuttle hypothesis, and further suggest that viral lysis of both autotrophic and heterotrophic prokaryotes may play a role in carbon export. Our analyses revealed the diversity and origins of prevalent viruses found on deep-sea sinking particles and identified prospective viral groups for future investigation into processes that govern particle export in the open ocean.
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Affiliation(s)
- Elaine Luo
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawai'i at Manoa, Honolulu, HI, 96822, USA.
- Woods Hole Oceanographic Institution, 266 Woods Hole Road, MS 51, Woods Hole MA, 02543, Falmouth, USA.
| | - Andy O Leu
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawai'i at Manoa, Honolulu, HI, 96822, USA
- Australia Center for Ecogenomics, University of Queensland, St. Lucia QLD, 4072, Australia
| | - John M Eppley
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawai'i at Manoa, Honolulu, HI, 96822, USA
| | - David M Karl
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawai'i at Manoa, Honolulu, HI, 96822, USA
| | - Edward F DeLong
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawai'i at Manoa, Honolulu, HI, 96822, USA.
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11
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Ebrahimi A, Goyal A, Cordero OX. Particle foraging strategies promote microbial diversity in marine environments. eLife 2022; 11:73948. [PMID: 35289269 PMCID: PMC8956285 DOI: 10.7554/elife.73948] [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] [Received: 09/16/2021] [Accepted: 03/01/2022] [Indexed: 11/26/2022] Open
Abstract
Microbial foraging in patchy environments, where resources are fragmented into particles or pockets embedded in a large matrix, plays a key role in natural environments. In the oceans and freshwater systems, particle-associated bacteria can interact with particle surfaces in different ways: some colonize only during short transients, while others form long-lived, stable colonies. We do not yet understand the ecological mechanisms by which both short- and long-term colonizers can coexist. Here, we address this problem with a mathematical model that explains how marine populations with different detachment rates from particles can stably coexist. In our model, populations grow only while on particles, but also face the increased risk of mortality by predation and sinking. Key to coexistence is the idea that detachment from particles modulates both net growth and mortality, but in opposite directions, creating a trade-off between them. While slow-detaching populations show the highest growth return (i.e., produce more net offspring), they are more susceptible to suffer higher rates of mortality than fast-detaching populations. Surprisingly, fluctuating environments, manifesting as blooms of particles (favoring growth) and predators (favoring mortality) significantly expand the likelihood that populations with different detachment rates can coexist. Our study shows how the spatial ecology of microbes in the ocean can lead to a predictable diversification of foraging strategies and the coexistence of multiple taxa on a single growth-limiting resource.
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Affiliation(s)
- Ali Ebrahimi
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, United States
| | - Akshit Goyal
- Department of Physics, Massachusetts Institute of Technology, Cambridge, United States
| | - Otto X Cordero
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, United States
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12
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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: 9] [Impact Index Per Article: 3.0] [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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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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14
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Acinas SG, Sánchez P, Salazar G, Cornejo-Castillo FM, Sebastián M, Logares R, Royo-Llonch M, Paoli L, Sunagawa S, Hingamp P, Ogata H, Lima-Mendez G, Roux S, González JM, Arrieta JM, Alam IS, Kamau A, Bowler C, Raes J, Pesant S, Bork P, Agustí S, Gojobori T, Vaqué D, Sullivan MB, Pedrós-Alió C, Massana R, Duarte CM, Gasol JM. Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities. Commun Biol 2021; 4:604. [PMID: 34021239 PMCID: PMC8139981 DOI: 10.1038/s42003-021-02112-2] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 04/16/2021] [Indexed: 02/04/2023] Open
Abstract
The deep sea, the largest ocean's compartment, drives planetary-scale biogeochemical cycling. Yet, the functional exploration of its microbial communities lags far behind other environments. Here we analyze 58 metagenomes from tropical and subtropical deep oceans to generate the Malaspina Gene Database. Free-living or particle-attached lifestyles drive functional differences in bathypelagic prokaryotic communities, regardless of their biogeography. Ammonia and CO oxidation pathways are enriched in the free-living microbial communities and dissimilatory nitrate reduction to ammonium and H2 oxidation pathways in the particle-attached, while the Calvin Benson-Bassham cycle is the most prevalent inorganic carbon fixation pathway in both size fractions. Reconstruction of the Malaspina Deep Metagenome-Assembled Genomes reveals unique non-cyanobacterial diazotrophic bacteria and chemolithoautotrophic prokaryotes. The widespread potential to grow both autotrophically and heterotrophically suggests that mixotrophy is an ecologically relevant trait in the deep ocean. These results expand our understanding of the functional microbial structure and metabolic capabilities of the largest Earth aquatic ecosystem.
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Affiliation(s)
- Silvia G Acinas
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain.
| | - Pablo Sánchez
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain
| | - Guillem Salazar
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, Zurich, Switzerland
| | - Francisco M Cornejo-Castillo
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain
- Department of Ocean Sciences, University of California, Santa Cruz, CA, USA
| | - Marta Sebastián
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain
- Instituto de Oceanografía y Cambio Global, IOCAG, Universidad de Las Palmas de Gran Canaria, ULPGC, Gran Canaria, Spain
| | - Ramiro Logares
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain
| | - Marta Royo-Llonch
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain
| | - Lucas Paoli
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, Zurich, Switzerland
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, Zurich, Switzerland
| | - Pascal Hingamp
- Aix Marseille Univ., Université de Toulon, CNRS, Marseille, France
| | - Hiroyuki Ogata
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Japan
| | - Gipsi Lima-Mendez
- Cellular and Molecular Microbiology, Faculté des Sciences, Université libre de Bruxelles (ULB), Brussels, Belgium
- Interuniversity Institute for Bioinformatics in Brussels, ULB-VUB, Brussels, Belgium
| | - Simon Roux
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
- U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - José M González
- Department of Microbiology, University of La Laguna, La Laguna, Spain
| | - Jesús M Arrieta
- Spanish Institute of Oceanography (IEO), Oceanographic Center of The Canary Islands, Dársena Pesquera, Santa Cruz de Tenerife, Spain
| | - Intikhab S Alam
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, Saudi Arabia
| | - Allan Kamau
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, Saudi Arabia
| | - Chris Bowler
- Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, Paris, France
| | - Jeroen Raes
- Department of Microbiology and Immunology, Rega Institute, KU Leuven - University of Leuven, Leuven, Belgium
- VIB Center for Microbiology, Leuven, Belgium
| | - Stéphane Pesant
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- PANGAEA, Data Publisher for Earth and Environmental Science, University of Bremen, Bremen, Germany
| | - Peer Bork
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Susana Agustí
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC), Thuwal, Saudi Arabia
| | - Takashi Gojobori
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, Saudi Arabia
| | - Dolors Vaqué
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain
| | - Matthew B Sullivan
- Department of Microbiology and Civil Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH, USA
| | - Carlos Pedrós-Alió
- Department of Systems Biology, Centro Nacional de Biotecnología (CNB), CSIC, Madrid, Spain
| | - Ramon Massana
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain
| | - Carlos M Duarte
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC) and Computational Bioscience Research Center (CBRC), Thuwal, Saudi Arabia
| | - Josep M Gasol
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain
- Centre for Marine Ecosystems Research, School of Sciences, Edith Cowan University, Joondalup, WA, Australia
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15
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Liu Y, Lin Q, Feng J, Yang F, Du H, Hu Z, Wang H. Differences in metabolic potential between particle-associated and free-living bacteria along Pearl River Estuary. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 728:138856. [PMID: 32570327 DOI: 10.1016/j.scitotenv.2020.138856] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 04/15/2020] [Accepted: 04/19/2020] [Indexed: 06/11/2023]
Abstract
Particulate organic matter (POM) in aquatic ecosystem is critical for biogeochemical cycling and host distinct communities of microbes, compared to its surrounding water. In this study, the structures and functional potentials of microbial communities associated with particles or free-living in water samples from the Pearl River Estuary were investigated using 16S rRNA gene sequencing and GeoChip 5.0 analysis. Significant differences in the community structure and genetic functional potentials between particle-associated bacteria and free-living bacteria were observed across all eight sampling sites. In particle-associated bacteria communities, Rhodobacteraceae and Flavobacteriaceae were more abundant, while SAR11 clade and SAR86 clade were the most abundant in free-living bacteria communities. The richness and abundance of functional genes involved in nutrient cycling and stress response, including carbon degradation, nitrogen fixation, DMSP degradation, and polyphosphate degradation, were much higher in particle-associated bacteria compared with free-living bacteria. Thus, the particle-associated bacteria seem to play a much more important role in the biogeochemical cycles than free-living bacteria. In conclusion, the results from this study highlight the central role played by particle-associated bacteria in structuring microbial assemblages, and their importance for mediating biogeochemical cycling in the estuarine ecosystem.
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Affiliation(s)
- Yanyang Liu
- Biology Department, College of Science, Shantou University, Shantou 515063, China; Institute of Marine Sciences, Shantou University, Shantou 515063, China; Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China
| | - Qun Lin
- Biology Department, College of Science, Shantou University, Shantou 515063, China; Institute of Marine Sciences, Shantou University, Shantou 515063, China; Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China
| | - Jiarong Feng
- Biology Department, College of Science, Shantou University, Shantou 515063, China; Institute of Marine Sciences, Shantou University, Shantou 515063, China; Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China
| | - Fumin Yang
- Biology Department, College of Science, Shantou University, Shantou 515063, China; Institute of Marine Sciences, Shantou University, Shantou 515063, China; Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China
| | - Hong Du
- Biology Department, College of Science, Shantou University, Shantou 515063, China; Institute of Marine Sciences, Shantou University, Shantou 515063, China; Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China
| | - Zhong Hu
- Biology Department, College of Science, Shantou University, Shantou 515063, China; Institute of Marine Sciences, Shantou University, Shantou 515063, China; Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China
| | - Hui Wang
- Biology Department, College of Science, Shantou University, Shantou 515063, China; Institute of Marine Sciences, Shantou University, Shantou 515063, China; Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China.
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16
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Lifestyle preferences drive the structure and diversity of bacterial and archaeal communities in a small riverine reservoir. Sci Rep 2020; 10:11288. [PMID: 32647153 PMCID: PMC7347578 DOI: 10.1038/s41598-020-67774-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 04/22/2020] [Indexed: 02/01/2023] Open
Abstract
Spatial heterogeneity along river networks is interrupted by dams, affecting the transport, processing, and storage of organic matter, as well as the distribution of biota. We here investigated the structure of planktonic (free-living, FL), particle-attached (PA) and sediment-associated (SD) bacterial and archaeal communities within a small reservoir. We combined targeted-amplicon sequencing of bacterial and archaeal 16S rRNA genes in the DNA and RNA community fractions from FL, PA and SD, followed by imputed functional metagenomics, in order to unveil differences in their potential metabolic capabilities within the reservoir (tail, mid, and dam sections) and lifestyles (FL, PA, SD). Both bacterial and archaeal communities were structured according to their life-style preferences rather than to their location in the reservoir. Bacterial communities were richer and more diverse when attached to particles or inhabiting the sediment, while Archaea showed an opposing trend. Differences between PA and FL bacterial communities were consistent at functional level, the PA community showing higher potential capacity to degrade complex carbohydrates, aromatic compounds, and proteinaceous materials. Our results stressed that particle-attached prokaryotes were phylogenetically and metabolically distinct from their free-living counterparts, and that performed as hotspots for organic matter processing within the small reservoir.
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17
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Shoemaker KM, Duhamel S, Moisander PH. Copepods promote bacterial community changes in surrounding seawater through farming and nutrient enrichment. Environ Microbiol 2019; 21:3737-3750. [PMID: 31222878 DOI: 10.1111/1462-2920.14723] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 05/21/2019] [Accepted: 06/18/2019] [Indexed: 12/11/2022]
Abstract
Bacteria living in the oligotrophic open ocean have various ways to survive under the pressure of nutrient limitation. Copepods, an abundant portion of the mesozooplankton, release nutrients through excretion and sloppy feeding that can support growth of surrounding bacteria. We conducted incubation experiments in the North Atlantic Subtropical Gyre to investigate the response of bacterial communities in the presence of copepods. Bacterial community composition and abundance measurements indicate that copepods have the potential to influence the microbial communities surrounding and associating with them - their 'zoosphere', in two ways. First, copepods may attract and support the growth of copiotrophic bacteria including representatives of Vibrionaceae, Oceanospirillales and Rhodobacteraceae in waters surrounding them. Second, copepods appear to grow specific groups of bacteria in or on the copepod body, particularly Flavobacteriaceae and Pseudoalteromonadaceae, effectively 'farming' them and subsequently releasing them. These distinct mechanisms provide a new view into how copepods may shape microbial communities in the open ocean. Microbial processes in the copepod zoosphere may influence estimates of oceanic bacterial biomass and in part control bacterial community composition and distribution in seawater.
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Affiliation(s)
- Katyanne M Shoemaker
- Department of Biology, University of Massachusetts Dartmouth, North Dartmouth, MA, 02747, USA
| | - Solange Duhamel
- Lamont-Doherty Earth Observatory, Division of Biology and Paleo Environment, Columbia University, NY, 10964, USA
| | - Pia H Moisander
- Department of Biology, University of Massachusetts Dartmouth, North Dartmouth, MA, 02747, USA
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18
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Duret MT, Lampitt RS, Lam P. Prokaryotic niche partitioning between suspended and sinking marine particles. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:386-400. [PMID: 30246414 DOI: 10.1111/1758-2229.12692] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 09/12/2018] [Indexed: 06/08/2023]
Abstract
Suspended particles are major organic carbon substrates for heterotrophic microorganisms in the mesopelagic ocean (100-1000 m). Nonetheless, communities associated with these particles have been overlooked compared with sinking particles, the latter generally considered as main carbon transporters to the deep ocean. This study is the first to differentiate prokaryotic communities associated with suspended and sinking particles, collected with a marine snow catcher at four environmentally distinct stations in the Scotia Sea. Amplicon sequencing of 16S rRNA gene revealed distinct prokaryotic communities associated with the two particle-types in the mixed-layer (0-100 m) and upper-mesopelagic zone (mean dissimilarity 42.5% ± 15.2%). Although common remineralising taxa were present within both particle-types, gammaproteobacterial Pseudomonadales and Vibrionales, and alphaproteobacterial Rhodobacterales were found enriched in sinking particles up to 32-fold, while Flavobacteriales (Bacteroidetes) favoured suspended particles. We propose that this niche-partitioning may be driven by organic matter properties found within both particle-types: K-strategists, specialised in the degradation of complex organic compounds, thrived on semi-labile suspended particles, while generalists r-strategists were adapted to the transient labile organic contents of sinking particles. Differences between the two particle-associated communities were more pronounced in the mesopelagic than in the surface ocean, likely resulting from exchanges between particle-pools enabled by the stronger turbulence.
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Affiliation(s)
- Manon T Duret
- Ocean and Earth Science, University of Southampton, Southampton, UK
| | | | - Phyllis Lam
- Ocean and Earth Science, University of Southampton, Southampton, UK
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19
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Biological composition and microbial dynamics of sinking particulate organic matter at abyssal depths in the oligotrophic open ocean. Proc Natl Acad Sci U S A 2019; 116:11824-11832. [PMID: 31127042 PMCID: PMC6575173 DOI: 10.1073/pnas.1903080116] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Sinking particles composed of both organic and inorganic material feed the deep-sea ecosystem and contribute centrally to ocean carbon sequestration. Despite their importance, little is known about the biological composition of sinking particles reaching the deep sea. Time-series analyses of sinking particles unexpectedly revealed bacterial assemblages that were simple and homogeneous over time. Particle-associated eukaryote assemblages, however, were more variable and complex. Several modes of export were observed, including summer inputs from the surface, more stochastic export of surface-derived protists and animals, and contributions from midwater animals and deep-sea bacteria. In summary, sinking particles exhibited temporally variable, heterogeneous biological sources and activities that reflected their important roles in the downward transport and transformation of organic matter in the deep sea. Sinking particles are a critical conduit for the export of organic material from surface waters to the deep ocean. Despite their importance in oceanic carbon cycling and export, little is known about the biotic composition, origins, and variability of sinking particles reaching abyssal depths. Here, we analyzed particle-associated nucleic acids captured and preserved in sediment traps at 4,000-m depth in the North Pacific Subtropical Gyre. Over the 9-month time-series, Bacteria dominated both the rRNA-gene and rRNA pools, followed by eukaryotes (protists and animals) and trace amounts of Archaea. Deep-sea piezophile-like Gammaproteobacteria, along with Epsilonproteobacteria, comprised >80% of the bacterial inventory. Protists (mostly Rhizaria, Syndinales, and ciliates) and metazoa (predominantly pelagic mollusks and cnidarians) were the most common sinking particle-associated eukaryotes. Some near-surface water-derived eukaryotes, especially Foraminifera, Radiolaria, and pteropods, varied greatly in their abundance patterns, presumably due to sporadic export events. The dominance of piezophile-like Gammaproteobacteria and Epsilonproteobacteria, along with the prevalence of their nitrogen cycling-associated gene transcripts, suggested a central role for these bacteria in the mineralization and biogeochemical transformation of sinking particulate organic matter in the deep ocean. Our data also reflected several different modes of particle export dynamics, including summer export, more stochastic inputs from the upper water column by protists and pteropods, and contributions from sinking mid- and deep-water organisms. In total, our observations revealed the variable and heterogeneous biological origins and microbial activities of sinking particles that connect their downward transport, transformation, and degradation to deep-sea biogeochemical processes.
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20
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Guevara Campoverde NC, Hassenrück C, Buttigieg PL, Gärdes A. Characterization of bacterioplankton communities and quantification of organic carbon pools off the Galapagos Archipelago under contrasting environmental conditions. PeerJ 2018; 6:e5984. [PMID: 30533298 PMCID: PMC6282939 DOI: 10.7717/peerj.5984] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Accepted: 10/22/2018] [Indexed: 12/14/2022] Open
Abstract
Bacteria play a crucial role in the marine carbon cycle, contributing to the production and degradation of organic carbon. Here, we investigated organic carbon pools, aggregate formation, and bacterioplankton communities in three contrasting oceanographic settings in the Galapagos Archipelago. We studied a submarine CO2 vent at Roca Redonda (RoR), an upwelling site at Bolivar Channel (BoC) subjected to a weak El Niño event at the time of sampling in October 2014, as well as a site without volcanic or upwelling influence at Cowley Islet (CoI). We recorded physico-chemical parameters, and quantified particulate and dissolved organic carbon, transparent exopolymeric particles, and the potential of the water to form larger marine aggregates. Free-living and particle-attached bacterial communities were assessed via 16S rRNA gene sequencing. Both RoR and BoC exhibited temperatures elevated by 1–1.5 °C compared to CoI. RoR further experienced reduced pH between 6.8 and 7.4. We observed pronounced differences in organic carbon pools at each of the three sites, with highest dissolved organic carbon concentrations at BoC and RoR, and highest particulate organic carbon concentrations and aggregate formation at BoC. Bacterioplankton communities at BoC were dominated by opportunistic copiotrophic taxa, such as Alteromonas and Roseobacter, known to thrive in phytoplankton blooms, as opposed to oligotrophic taxa dominating at CoI, such as members of the SAR11 clade. Therefore, we propose that bacterial communities were mainly influenced by the availability of organic carbon at the investigated sites. Our study provides a comprehensive characterization of organic carbon pools and bacterioplankton communities, highlighting the high heterogeneity of various components of the marine carbon cycle around the Galapagos Archipelago.
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Affiliation(s)
- Nataly Carolina Guevara Campoverde
- Galapagos Science Center, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador.,Tropical Marine Microbiology, Department of Biogeochemistry and Geology, Leibniz-Centre for Tropical Marine Reseach, Bremen, Germany
| | - Christiane Hassenrück
- Tropical Marine Microbiology, Department of Biogeochemistry and Geology, Leibniz-Centre for Tropical Marine Reseach, Bremen, Germany
| | - Pier Luigi Buttigieg
- HGF-MPG Group for Deep Sea Ecology and Technology, Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
| | - Astrid Gärdes
- Tropical Marine Microbiology, Department of Biogeochemistry and Geology, Leibniz-Centre for Tropical Marine Reseach, Bremen, Germany
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21
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Wiegand S, Jogler M, Jogler C. On the maverick Planctomycetes. FEMS Microbiol Rev 2018; 42:739-760. [DOI: 10.1093/femsre/fuy029] [Citation(s) in RCA: 134] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 07/22/2018] [Indexed: 01/01/2023] Open
Affiliation(s)
- Sandra Wiegand
- Department of Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen, The Netherlands
| | - Mareike Jogler
- Leibniz Institute DSMZ, Inhoffenstraße 7b, 38124 Braunschweig, Germany
| | - Christian Jogler
- Department of Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen, The Netherlands
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Haro-Moreno JM, López-Pérez M, de la Torre JR, Picazo A, Camacho A, Rodriguez-Valera F. Fine metagenomic profile of the Mediterranean stratified and mixed water columns revealed by assembly and recruitment. MICROBIOME 2018; 6:128. [PMID: 29991350 PMCID: PMC6040077 DOI: 10.1186/s40168-018-0513-5] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 07/02/2018] [Indexed: 05/07/2023]
Abstract
BACKGROUND The photic zone of aquatic habitats is subjected to strong physicochemical gradients. To analyze the fine-scale variations in the marine microbiome, we collected seven samples from a single offshore location in the Mediterranean at 15 m depth intervals during a period of strong stratification, as well as two more samples during the winter when the photic water column was mixed. We were able to recover 94 new metagenome-assembled genomes (MAGs) from these metagenomes and examine the distribution of key marine microbes within the photic zone using metagenomic recruitment. RESULTS Our results showed significant differences in the microbial composition of different layers within the stratified photic water column. The majority of microorganisms were confined to discreet horizontal layers of no more than 30 m (stenobathic). Only a few such as members of the SAR11 clade appeared at all depths (eurybathic). During the winter mixing period, only some groups of bloomers such as Pseudomonas were favored. Although most microbes appeared in both seasons, some groups like the SAR116 clade and some Bacteroidetes and Verrucomicrobia seemed to disappear during the mixing period. Furthermore, we found that some microbes previously considered seasonal (e.g., Archaea or Actinobacteria) were living in deeper layers within the photic zone during the stratification period. A strong depth-related specialization was detected, not only at the taxonomic level but also at the functional level, even within the different clades, for the manipulation and uptake of specific polysaccharides. Rhodopsin sequences (green or blue) also showed narrow depth distributions that correlated with the taxonomy of the microbe in which they were found but not with depth. CONCLUSIONS Although limited to a single location in the Mediterranean, this study has profound implications for our understanding of how marine microbial communities vary with depth within the photic zone when stratified. Our results highlight the importance of collecting samples at different depths in the water column when comparing seasonal variations and have important ramifications for global marine studies that most often take samples from only one single depth. Furthermore, our perspective and approaches (metagenomic assembly and recruitment) are broadly applicable to other metagenomic studies.
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Affiliation(s)
- Jose M Haro-Moreno
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Apartado 18, San Juan de Alicante, 03550, Alicante, Spain
| | - Mario López-Pérez
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Apartado 18, San Juan de Alicante, 03550, Alicante, Spain
| | - José R de la Torre
- Department of Biology, San Francisco State University, San Francisco, CA, 94132, USA
| | - Antonio Picazo
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Burjassot, E-46100, Valencia, Spain
| | - Antonio Camacho
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Burjassot, E-46100, Valencia, Spain
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Apartado 18, San Juan de Alicante, 03550, Alicante, Spain.
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López-Pérez M, Haro-Moreno JM, Gonzalez-Serrano R, Parras-Moltó M, Rodriguez-Valera F. Genome diversity of marine phages recovered from Mediterranean metagenomes: Size matters. PLoS Genet 2017; 13:e1007018. [PMID: 28945750 PMCID: PMC5628999 DOI: 10.1371/journal.pgen.1007018] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 10/05/2017] [Accepted: 09/13/2017] [Indexed: 11/18/2022] Open
Abstract
Marine viruses play a critical role not only in the global geochemical cycles but also in the biology and evolution of their hosts. Despite their importance, viral diversity remains underexplored mostly due to sampling and cultivation challenges. Direct sequencing approaches such as viromics has provided new insights into the marine viral world. As a complementary approach, we analysed 24 microbial metagenomes (>0.2 μm size range) obtained from six sites in the Mediterranean Sea that vary by depth, season and filter used to retrieve the fraction. Filter-size comparison showed a significant number of viral sequences that were retained on the larger-pore filters and were different from those found in the viral fraction from the same sample, indicating that some important viral information is missing using only assembly from viromes. Besides, we were able to describe 1,323 viral genomic fragments that were more than 10Kb in length, of which 36 represented complete viral genomes including some of them retrieved from a cross-assembly from different metagenomes. Host prediction based on sequence methods revealed new phage groups belonging to marine prokaryotes like SAR11, Cyanobacteria or SAR116. We also identified the first complete virophage from deep seawater and a new endemic clade of the recently discovered Marine group II Euryarchaeota virus. Furthermore, analysis of viral distribution using metagenomes and viromes indicated that most of the new phages were found exclusively in the Mediterranean Sea and some of them, mostly the ones recovered from deep metagenomes, do not recruit in any database probably indicating higher variability and endemicity in Mediterranean bathypelagic waters. Together these data provide the first detailed picture of genomic diversity, spatial and depth variations of viral communities within the Mediterranean Sea using metagenome assembly.
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Affiliation(s)
- Mario López-Pérez
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Campus de San Juan, San Juan de Alicante, Spain
| | - Jose M. Haro-Moreno
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Campus de San Juan, San Juan de Alicante, Spain
| | - Rafael Gonzalez-Serrano
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Campus de San Juan, San Juan de Alicante, Spain
| | - Marcos Parras-Moltó
- Centro de Biología Molecular 'Severo Ochoa' (Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid), Cantoblanco, Madrid, Spain
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Campus de San Juan, San Juan de Alicante, Spain
- * E-mail:
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Morphological Identification and Single-Cell Genomics of Marine Diplonemids. Curr Biol 2016; 26:3053-3059. [DOI: 10.1016/j.cub.2016.09.013] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 08/25/2016] [Accepted: 09/07/2016] [Indexed: 11/19/2022]
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