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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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Lekired A, Cherif-Silini H, Silini A, Ben Yahia H, Ouzari HI. Comparative genomics reveals the acquisition of mobile genetic elements by the plant growth-promoting Pantoea eucrina OB49 in polluted environments. Genomics 2023; 115:110579. [PMID: 36792019 DOI: 10.1016/j.ygeno.2023.110579] [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: 06/17/2022] [Revised: 02/08/2023] [Accepted: 02/09/2023] [Indexed: 02/15/2023]
Abstract
Heavy metal-tolerant plant growth-promoting bacteria (PGPB) have gained popularity in bioremediation in recent years. A genome-assisted study of a heavy metal-tolerant PGPB Pantoea eucrina OB49 isolated from the rhizosphere of wheat grown on a heavy metal-contaminated site is presented. Comparative pan-genome analysis indicated that OB49 acquired heavy metal resistance genes through horizontal gene transfer. On contigs S10 and S12, OB49 has two arsRBCH operons that give arsenic resistance. On the S12 contig, an arsRBCH operon was discovered in conjunction with the merRTPCADE operon, which provides mercury resistance. P. eucrina OB49 may be involved in an ecological alternative for heavy metal remediation and growth promotion of wheat grown in metal-polluted soils. Our results suggested the detection of mobile genetic elements that harbour the ars operon and the fluoride resistance genes adjacent to the mer operon.
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Affiliation(s)
- Abdelmalek Lekired
- Laboratory of Microorganisms and Active Biomolecules, MBA-LR03ES03, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Hafsa Cherif-Silini
- Laboratory of Applied Microbiology, Department of Microbiology, Faculty of Natural and Life Sciences, Ferhat Abbas University, 19000, Setif, Algeria
| | - Allaoua Silini
- Laboratory of Applied Microbiology, Department of Microbiology, Faculty of Natural and Life Sciences, Ferhat Abbas University, 19000, Setif, Algeria
| | - Hamza Ben Yahia
- Laboratory of Microorganisms and Active Biomolecules, MBA-LR03ES03, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Hadda-Imene Ouzari
- Laboratory of Microorganisms and Active Biomolecules, MBA-LR03ES03, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis, Tunisia.
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Quintero IJ, Castillo AM, Mejía LC. Diversity and Taxonomy of Soil Bacterial Communities in Urban and Rural Mangrove Forests of the Panama Bay. Microorganisms 2022; 10:microorganisms10112191. [PMID: 36363784 PMCID: PMC9697262 DOI: 10.3390/microorganisms10112191] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 10/26/2022] [Accepted: 10/27/2022] [Indexed: 11/09/2022] Open
Abstract
Mangrove ecosystems are threatened worldwide by a wide range of factors including climate change, coastal development, and pollution. The effects of these factors on soil bacterial communities of Neotropical mangroves and their temporal dynamics is largely undocumented. Here we compared the diversity and taxonomic composition of bacterial communities in the soil of two mangrove forest sites of the Panama Bay: Juan Diaz (JD), an urban mangrove forest in Panama City surrounded by urban development, with occurrence of five mangrove species, and polluted with solid waste and sewage; and Bayano (B), a rural mangrove forest without urban development, without solid waste pollution, and with the presence of two mangrove species. Massive amplicon sequencing of the V4 region of the 16S rRNA gene and community analyses were implemented. In total, 20,691 bacterial amplicon sequence variants were identified, and the bacterial community was more diverse in the rural mangrove forest based on Faith’s phylogenetic diversity index. The three dominant phyla of bacteria found and shared between the two sites were Proteobacteria, Desulfobacterota, and Chloroflexi. The ammonia oxidizing archaea class Nitrosphaeria was found among the top 10 most abundant. Dominant genera of bacteria that occurred in the two mangrove sites were: BD2-11_terrestrial_group (Gemmatimonadota), EPR3968-O8a-Bc78 (Gammaproteobacteria), Salinimicrobium (Bacteroidetes), Sulfurovum (Campylobacteria), and Woeseia (Gammaproteobacteria) of which the first three and Methyloceanibacter had increased in relative abundance in the transition from rainy to dry to rainy season in the urban mangrove forest. Altogether, our study suggests that factors such as urban development, vegetation composition, pollution, and seasonal changes may cause shifts in bacterial diversity and relative abundance of specific taxa in mangrove soils. In particular, taxa with roles in biogeochemical cycles of carbon, nitrogen, sulfur, and phosphorus, and on rhizosphere taxa, could be important for mangrove plant resilience to environmental stress.
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Affiliation(s)
- Indira J. Quintero
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT-AIP) Clayton, Panamá 0843, Panama
- Programa de Maestría en Ciencias Biológicas, Universidad de Panamá, Panamá 0824, Panama
| | - Anakena M. Castillo
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT-AIP) Clayton, Panamá 0843, Panama
- Departamento de Investigación en Entomología Médica, Instituto Conmemorativo Gorgas de Estudios de la Salud (ICGES), Panamá 0816, Panama
| | - Luis C. Mejía
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT-AIP) Clayton, Panamá 0843, Panama
- Smithsonian Tropical Research Institute, Panamá 0843, Panama
- Departamento de Genética y Biología Molecular, Universidad de Panamá, Panamá 0824, Panama
- Correspondence: ; Tel.: +507-517-0700
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Taketani RG, Dini-Andreote F, Beier S, Fernandez C. Editorial: Advancements in the Understanding of Anthropogenic Impacts on the Microbial Ecology and Function of Aquatic Environments. Front Microbiol 2022; 12:820697. [PMID: 35140699 PMCID: PMC8818849 DOI: 10.3389/fmicb.2021.820697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 12/15/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Rodrigo G. Taketani
- Sustainable Agriculture Sciences. Rothamsted Research, Harpenden, United Kingdom
- *Correspondence: Rodrigo G. Taketani
| | - Francisco Dini-Andreote
- Department of Plant Science & Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, United States
| | - Sara Beier
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research, Warnemünde, Germany
| | - Camila Fernandez
- LOMIC UMR7621 CNRS Observatoire Oceanologique de Banyuls sur Mer, Languedoc-Roussillon, France
- COPAS SUR AUSTRAL, COPAS COASTAL, INCAR Center, Universidad de Concepcion, Concepción, Chile
- IDEAL Center, Universidad Austral, Valdivia, Chile
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Zhang CJ, Chen YL, Sun YH, Pan J, Cai MW, Li M. Diversity, metabolism and cultivation of archaea in mangrove ecosystems. MARINE LIFE SCIENCE & TECHNOLOGY 2021; 3:252-262. [PMID: 37073347 PMCID: PMC10077227 DOI: 10.1007/s42995-020-00081-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 10/19/2020] [Indexed: 05/03/2023]
Abstract
Mangroves comprise a globally significant intertidal ecosystem that contains a high diversity of microorganisms, including fungi, bacteria and archaea. Archaea is a major domain of life that plays important roles in biogeochemical cycles in these ecosystems. In this review, the potential roles of archaea in mangroves are briefly highlighted. Then, the diversity and metabolism of archaeal community of mangrove ecosystems across the world are summarized and Bathyarchaeota, Euryarchaeota, Thaumarchaeota, Woesearchaeota, and Lokiarchaeota are confirmed as the most abundant and ubiquitous archaeal groups. The metabolic potential of these archaeal groups indicates their important ecological function in carbon, nitrogen and sulfur cycling. Finally, some cultivation strategies that could be applied to uncultivated archaeal lineages from mangrove wetlands are suggested, including refinements to traditional cultivation methods based on genomic and transcriptomic information, and numerous innovative cultivation techniques such as single-cell isolation and high-throughput culturing (HTC). These cultivation strategies provide more opportunities to obtain previously uncultured archaea.
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Affiliation(s)
- Cui-Jing Zhang
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060 China
| | - Yu-Lian Chen
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060 China
| | - Yi-Hua Sun
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060 China
| | - Jie Pan
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060 China
| | - Ming-Wei Cai
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060 China
| | - Meng Li
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060 China
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do Carmo Linhares D, Saia FT, Duarte RTD, Nakayama CR, de Melo IS, Pellizari VH. Methanotrophic Community Detected by DNA-SIP at Bertioga's Mangrove Area, Southeast Brazil. MICROBIAL ECOLOGY 2021; 81:954-964. [PMID: 33392629 DOI: 10.1007/s00248-020-01659-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 12/03/2020] [Indexed: 06/12/2023]
Abstract
Methanotrophic bacteria can use methane as sole carbon and energy source. Its importance in the environment is related to the mitigation of methane emissions from soil and water to the atmosphere. Brazilian mangroves are highly productive, have potential to methane production, and it is inferred that methanotrophic community is of great importance for this ecosystem. The scope of this study was to investigate the functional and taxonomic diversity of methanotrophic bacteria present in the anthropogenic impacted sediments from Bertioga´s mangrove (SP, Brazil). Sediment sample was cultivated with methane and the microbiota actively involved in methane oxidation was identified by DNA-based stable isotope probing (DNA-SIP) using methane as a labeled substrate. After 4 days (96 h) of incubation and consumption of 0.7 mmol of methane, the most active microorganisms were related to methanotrophs Methylomonas and Methylobacter as well as to methylotrophic Methylotenera, indicating a possible association of these bacterial groups within a methane-derived food chain in the Bertioga mangrove. The abundance of genera Methylomonas, able to couple methane oxidation to nitrate reduction, may indicate that under low dissolved oxygen tensions, some aerobic methanotrophs could shift to intraerobic methane oxidation to avoid oxygen starvation.
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Affiliation(s)
- Débora do Carmo Linhares
- Laboratory of Industrial Biotechnology, Institute for Technological Research of São Paulo, 05508-901, São Paulo, SP, Brazil.
- Department of Biological Oceanography, Oceanographic Institute, University of Sao Paulo, Praça do Oceanográfico, 191, 05508-120, Butantã, São Paulo-SP, Brazil.
| | - Flávia Talarico Saia
- Institute of Marine Sciences, Federal University of São Paulo, Av. Dr. Carvalho de Mendonça, 144, Encruzilhada, Santos, SP, 11070-102, Brazil
| | - Rubens Tadeu Delgado Duarte
- Laboratory of Molecular Ecology and Extremophiles, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, 88040-900, Brazil
| | - Cristina Rossi Nakayama
- Institute of Environmental, Chemical and Pharmaceutical Sciences, Federal University of São Paulo, Rua São Nicolau, 210, Diadema, SP, 09913-030, Brazil
| | | | - Vivian Helena Pellizari
- Department of Biological Oceanography, Oceanographic Institute, University of Sao Paulo, Praça do Oceanográfico, 191, 05508-120, Butantã, São Paulo-SP, Brazil
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Bao H, Li Y, Diao X, Wang S. Effects of algal bloom (AB) on sediment microorganisms with special functions at different AB stages in Chaohu Lake. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2021; 83:1130-1140. [PMID: 33724942 DOI: 10.2166/wst.2021.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Algal bloom (AB) is a serious water environment problem in China, but it is still unclear how AB affects microorganisms with special functions (such as nitrogen-, phosphorus-, sulfur- and iron-related bacteria) at different AB stages. Samples of water and sediment were taken in the AB region and free algal bloom (FAB) region of Chaohu Lake at different AB stages, and the numbers of N-, P-, S- and Fe-related bacteria were determined by culture-dependent methods. Results showed that during the whole experiment, numbers of N-, P-, S-, and Fe-related bacteria in the AB region were significantly higher than those in the FAB region, especially at the AB outbreak stage. In the FAB region, numbers of above bacteria showed little variation with time. In the AB region, however, numbers of N-, S-, and Fe-related bacteria evidently changed as 'Λ'-type with AB process. They presented an upward trend at the AB formation stage and the initial stage of AB outbreak, and then showed a downward trend. Numbers of P-related bacteria also showed a similar trend as the above bacteria, but they kept high level for long time at the AB outbreak stage. This study indicated that AB produced different effects on microorganisms with special functions at different AB stages.
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Affiliation(s)
- Hongfu Bao
- Appraisal Center for Environment and Engineering, Ministry of Ecology and Environment, Beijing 100012, China
| | - Yiwei Li
- Chinese Research Academy of Environmental Sciences, Beijing, 100012, China E-mail:
| | - Xiaojun Diao
- Appraisal Center for Environment and Engineering, Ministry of Ecology and Environment, Beijing 100012, China
| | - Shuguang Wang
- Department of Environmental Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China; † Equivalent contribution author
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Li M, Mi T, He H, Chen Y, Zhen Y, Yu Z. Active bacterial and archaeal communities in coastal sediments: Biogeography pattern, assembly process and co-occurrence relationship. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 750:142252. [PMID: 33182220 DOI: 10.1016/j.scitotenv.2020.142252] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 08/12/2020] [Accepted: 09/05/2020] [Indexed: 06/11/2023]
Abstract
The biogeography of active microbial communities and the underlying mechanisms in marine sediments are important in microbial ecology but remain unclear. Here, using qPCR and high-throughput sequencing, we investigated bacterial and archaeal community abundances and activities by quantifying the abundance and expression of the 16S rRNA gene respectively, RNA-derived bacterial and archaeal community biogeography, assembly mechanisms and co-occurrence relationships in surface sediment samples from the Bohai Sea (BS), South Yellow Sea (SYS) and the north East China Sea (NECS) of the eastern Chinese marginal seas. The results revealed a higher heterogeneity of bacterial and archaeal community activities than of abundances and heterogeneous ecological functions among areas reflected by community compositions. Furthermore, clear geographic groups (i.e., the BS, SYS and NECS groups) were observed for all, abundant and rare active bacterial and archaeal communities, accompanied by significant distance-decay patterns. However, the abundant and rare taxa showed inconsistent geographic patterns. More importantly, deterministic processes played a greater role than stochastic processes in active bacterial and archaeal community assembly. The rare taxa had weaker abilities to disperse and/or adapt and more complex ecological processes than the abundant taxa. In addition, this study also showed that intertaxa competition was the dominant interaction between active bacterial and archaeal members, which could greatly contribute to dispersal limitation. Moreover, active bacterial and archaeal co-occurrence patterns showed significant distance-decay patterns, which were consistent with the community compositions.
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Affiliation(s)
- Mingyue Li
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China; Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China; Key Laboratory of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao 266100, China
| | - Tiezhu Mi
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China; Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China; Key Laboratory of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao 266100, China
| | - Hui He
- College of Marine Life Science, Ocean University of China, Qingdao 266003, China
| | - Ye Chen
- Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China; Key Laboratory of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao 266100, China; College of Marine Life Science, Ocean University of China, Qingdao 266003, China
| | - Yu Zhen
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China; Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China; Key Laboratory of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao 266100, China.
| | - Zhigang Yu
- Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China; Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education/Institute for Advanced Ocean Study, Ocean University of China, Qingdao 266100, China
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Mukherji S, Ghosh A, Bhattacharyya C, Mallick I, Bhattacharyya A, Mitra S, Ghosh A. Molecular and culture-based surveys of metabolically active hydrocarbon-degrading archaeal communities in Sundarban mangrove sediments. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 195:110481. [PMID: 32203775 DOI: 10.1016/j.ecoenv.2020.110481] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 02/21/2020] [Accepted: 03/13/2020] [Indexed: 06/10/2023]
Abstract
Archaea remain important players in global biogeochemical cycles worldwide, including in the highly productive mangrove estuarine ecosystems. In the present study, we have explored the diversity, distribution, and function of the metabolically active fraction of the resident archaeal community of the Sundarban mangrove ecosystem, using both culture-independent and culture-dependent approaches. To evaluate the diversity and distribution pattern of the active archaeal communities, RNA based analysis of the 16S rRNA gene was performed on an Illumina platform. The active Crenarchaeal community was observed to remain constant while active Euryarchaeal community underwent considerable change across the sampling sites depending on varying anthropogenic factors. Haloarchaea were the predominant group in hydrocarbon polluted sediments, leading us to successfully isolate eleven p-hydroxybenzoic acid degrading haloarchaeal species. The isolates could also survive in benzoic acid, naphthalene, and o-phthalate. Quantitative estimation of p-hydroxybenzoic acid degradation was studied on select isolates, and their ability to reduce COD of polluted saline waters of Sundarban was also evaluated. To our knowledge, this is the first ever study combining culture-independent (Next Generation sequencing and metatranscriptome) and culture-dependent analyses for an assessment of archaeal function in the sediment of Sundarban.
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Affiliation(s)
- Shayantan Mukherji
- Department of Biochemistry, Bose Institute, P1/12- C.I.T. Road, Scheme VIIM, Kolkata, 700054, West Bengal, India
| | - Anandita Ghosh
- Department of Biochemistry, Bose Institute, P1/12- C.I.T. Road, Scheme VIIM, Kolkata, 700054, West Bengal, India
| | - Chandrima Bhattacharyya
- Department of Biochemistry, Bose Institute, P1/12- C.I.T. Road, Scheme VIIM, Kolkata, 700054, West Bengal, India
| | - Ivy Mallick
- Department of Biochemistry, Bose Institute, P1/12- C.I.T. Road, Scheme VIIM, Kolkata, 700054, West Bengal, India
| | - Anish Bhattacharyya
- Department of Biochemistry, 35 Ballygunge Circular Road, University of Calcutta, Kolkata, 700019, India
| | - Suparna Mitra
- Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, Thoresby Place, Leeds, LS1 3EX, W. Yorkshire, United Kingdom
| | - Abhrajyoti Ghosh
- Department of Biochemistry, Bose Institute, P1/12- C.I.T. Road, Scheme VIIM, Kolkata, 700054, West Bengal, India.
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Ceccon DM, Faoro H, Lana PDC, Souza EMD, Pedrosa FDO. Metataxonomic and metagenomic analysis of mangrove microbiomes reveals community patterns driven by salinity and pH gradients in Paranaguá Bay, Brazil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 694:133609. [PMID: 31400683 DOI: 10.1016/j.scitotenv.2019.133609] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 05/18/2019] [Accepted: 07/25/2019] [Indexed: 06/10/2023]
Abstract
While environmental drivers regulate the structure of mangrove microbial communities, their exact nature and the extent of their influence require further elucidation. By means of 16S rRNA gene-based sequencing, we determined the microbial taxonomic profiles of mangroves in the subtropical Paranaguá Bay, Brazil, considering as potential drivers: salinity, as represented by two sectors in the extremes of a salinity gradient (<5 PSU and >30 PSU); proximity to/absence of the prevailing plants, Avicennia schaueriana, Laguncularia racemosa, Rhizophora mangle, and Spartina alterniflora; and the chemical composition of the sediments. Salinity levels within the estuary had the strongest influence on microbial structure, and pH was important to separate two communities within the high salinity environment. About one fourth of the total variation in community structure resulted from covariation of salinity and the overall chemical composition, which might indicate that the chemical profile was also related to salinity. The most prevalent bacterial phyla associated with the mangrove soils analyzed included Proteobacteria, Actinobacteria, Chloroflexi, Bacteroidetes, Acidobacteria, and Cyanobacteria. Taxonomic and functional comparisons of our results for whole-genome sequencing with available data from other biomes showed that the studied microbiomes cluster first according to biome type, then to matrix type and salinity status. Metabolic functions were more conserved than organisms within mangroves and across all biomes, indicating that core functions are preserved in any of the given conditions regardless of the specific organisms harboring them.
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Affiliation(s)
- Denny Marcel Ceccon
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Helisson Faoro
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Paulo da Cunha Lana
- Center for Marine Studies, Universidade Federal do Paraná, Pontal do Paraná, Brazil
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Moitinho MA, Chiaramonte JB, Souza DT, Solano JH, Bononi L, Melo IS, Taketani RG. Intraspecific variation on epiphytic bacterial community from Laguncularia racemosa phylloplane. Braz J Microbiol 2019; 50:1041-1050. [PMID: 31473927 PMCID: PMC6863213 DOI: 10.1007/s42770-019-00138-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 08/07/2019] [Indexed: 10/26/2022] Open
Abstract
Mangroves are dynamic and unique ecosystems that provide important ecological services to coastal areas. The phylloplane is one of the greatest microbial habitats, and most of its microorganisms are uncultivated under common laboratory conditions. Bacterial community structure of Laguncularia racemosa phylloplane, a well-adapted mangrove species with salt exudation at foliar levels, was accessed through 16S rRNA amplicon sequencing. Sampling was performed in three different sites across a transect from upland to the seashore in a preserved mangrove forest located in the city of Cananéia, São Paulo State, Brazil. Higher bacterial diversity was observed in intermediary locations between the upland and the seashore, showing that significant intraspecific spatial variation in bacterial communities exists between a single host species with the selection of specific population between an environmental transect.
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Affiliation(s)
- Marta A Moitinho
- Laboratory of Environmental Microbiology, Brazilian Agricultural Research Corporation, EMBRAPA Environment, SP 340. Highway-Km 127.5, Jaguariúna, SP, 13820-000, Brazil
- College of Agriculture Luiz de Queiroz, University of São Paulo, Pádua Dias Avenue, 11, Piracicaba, SP, 13418-900, Brazil
| | - Josiane B Chiaramonte
- Laboratory of Environmental Microbiology, Brazilian Agricultural Research Corporation, EMBRAPA Environment, SP 340. Highway-Km 127.5, Jaguariúna, SP, 13820-000, Brazil
- College of Agriculture Luiz de Queiroz, University of São Paulo, Pádua Dias Avenue, 11, Piracicaba, SP, 13418-900, Brazil
| | - Danilo T Souza
- Laboratory of Environmental Microbiology, Brazilian Agricultural Research Corporation, EMBRAPA Environment, SP 340. Highway-Km 127.5, Jaguariúna, SP, 13820-000, Brazil
| | - Juanita H Solano
- Laboratory of Environmental Microbiology, Brazilian Agricultural Research Corporation, EMBRAPA Environment, SP 340. Highway-Km 127.5, Jaguariúna, SP, 13820-000, Brazil
- College of Agriculture Luiz de Queiroz, University of São Paulo, Pádua Dias Avenue, 11, Piracicaba, SP, 13418-900, Brazil
| | - Laura Bononi
- Laboratory of Environmental Microbiology, Brazilian Agricultural Research Corporation, EMBRAPA Environment, SP 340. Highway-Km 127.5, Jaguariúna, SP, 13820-000, Brazil
- College of Agriculture Luiz de Queiroz, University of São Paulo, Pádua Dias Avenue, 11, Piracicaba, SP, 13418-900, Brazil
| | - Itamar S Melo
- Laboratory of Environmental Microbiology, Brazilian Agricultural Research Corporation, EMBRAPA Environment, SP 340. Highway-Km 127.5, Jaguariúna, SP, 13820-000, Brazil
| | - Rodrigo G Taketani
- College of Agriculture Luiz de Queiroz, University of São Paulo, Pádua Dias Avenue, 11, Piracicaba, SP, 13418-900, Brazil.
- CETEM, Centre for Mineral Technology, MCTIC Ministry of Science, Technology, Innovation and Communication, Cidade Universitária, Av. Pedro Calmon, 900, Cidade Universitária, Ilha do Fundão, Rio de Janeiro, ZC 21941-908, Brazil.
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Haleyur N, Shahsavari E, Jain SS, Koshlaf E, Ravindran VB, Morrison PD, Osborn AM, Ball AS. Influence of bioaugmentation and biostimulation on PAH degradation in aged contaminated soils: Response and dynamics of the bacterial community. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 238:49-58. [PMID: 30844545 DOI: 10.1016/j.jenvman.2019.02.115] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 01/31/2019] [Accepted: 02/25/2019] [Indexed: 06/09/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) represent a group of hazardous compounds that are ubiquitous and persistent. The main aim of this study was to investigate the degradation of PAHs in chronically contaminated, aged and weathered soils obtained from a former gas plant of Australia. Biostimulation and bioaugmentation using individual isolates (Rhodococcus sp. (NH2), Achromobacter sp. (NH13), Oerskovia paurometabola (NH11), Pantoea sp. (NH15), Sejongia sp. (NH20), Microbacterium maritypicum (NH30) and Arthrobacter equi (NH21)) and a consortium of these isolates were tested during mesocosm studies. A significant reduction (99%) in PAH concentration was observed in all the treatments. In terms of the abundance of PAH-degrading genes and microbial community structure during PAH degradation, qPCR results revealed that Gram-positive bacteria were dominant over other bacterial communities in all the treatments. 16S sequencing results revealed that the inoculated organisms did not establish themselves during the treatment. However, substantial bacterial community changes during the treatments were observed, suggesting that the natural community exhibited sufficient resilience and diversity to enable an active, but changing degrading community at all stages of the degradation process. Consequently, biostimulation is proposed as the best strategy to remediate PAHs in aged, weathered and chronically contaminated soils.
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Affiliation(s)
- Nagalakshmi Haleyur
- School of Science, RMIT University, Bundoora, Melbourne, VIC, 3083, Australia; Centre for Environmental Sustainability and Remediation, RMIT University, Bundoora, Melbourne, VIC, 3083, Australia.
| | - Esmaeil Shahsavari
- School of Science, RMIT University, Bundoora, Melbourne, VIC, 3083, Australia; Centre for Environmental Sustainability and Remediation, RMIT University, Bundoora, Melbourne, VIC, 3083, Australia
| | - Sohni Singh Jain
- Department of Electrical and Biomedical Engineering, School of Engineering, RMIT University, Bundoora West, VIC, 3083, Australia
| | - Eman Koshlaf
- School of Science, RMIT University, Bundoora, Melbourne, VIC, 3083, Australia; Centre for Environmental Sustainability and Remediation, RMIT University, Bundoora, Melbourne, VIC, 3083, Australia
| | - Vivek B Ravindran
- School of Science, RMIT University, Bundoora, Melbourne, VIC, 3083, Australia; Centre for Environmental Sustainability and Remediation, RMIT University, Bundoora, Melbourne, VIC, 3083, Australia
| | - Paul D Morrison
- Centre for Environmental Sustainability and Remediation, RMIT University, Bundoora, Melbourne, VIC, 3083, Australia
| | - A Mark Osborn
- School of Science, RMIT University, Bundoora, Melbourne, VIC, 3083, Australia; Centre for Environmental Sustainability and Remediation, RMIT University, Bundoora, Melbourne, VIC, 3083, Australia
| | - Andrew S Ball
- School of Science, RMIT University, Bundoora, Melbourne, VIC, 3083, Australia; Centre for Environmental Sustainability and Remediation, RMIT University, Bundoora, Melbourne, VIC, 3083, Australia.
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Li Y, Zheng L, Zhang Y, Liu H, Jing H. Comparative metagenomics study reveals pollution induced changes of microbial genes in mangrove sediments. Sci Rep 2019; 9:5739. [PMID: 30952929 PMCID: PMC6450915 DOI: 10.1038/s41598-019-42260-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 03/26/2019] [Indexed: 01/21/2023] Open
Abstract
Mangrove forests are widespread along the subtropical and tropical coasts. They provide a habitat for a wide variety of plants, animals and microorganisms, and act as a buffer zone between the ocean and land. Along with other coastal environments, mangrove ecosystems are under increasing pressure from human activities, such as excessive input of nutrients and toxic pollutants. Despite efforts to understand the diversity of microbes in mangrove sediments, their metabolic capability in pristine and contaminated mangrove sediments remains largely unknown. By using metagenomic approach, we investigated the metabolic capacity of microorganisms in contaminated (CMS) and pristine (PMS) mangrove sediments at subtropical and tropical coastal sites. When comparing the CMS with PMS, we found that the former had a reduced diazotroph abundance and nitrogen fixing capability, but an enhanced metabolism that is related to the generation of microbial greenhouse gases via increased methanogenesis and sulfate reduction. In addition, a high concentration of heavy metals (mainly Zn, Cd, and Pb) and abundance of metal/antibiotic resistance encoding genes were found in CMS. Together, these data provide evidence that contamination in mangrove sediment can markedly change microbial community and metabolism; however, no significant differences in gene distribution were found between the subtropical and tropical mangrove sediments. In summary, contamination in mangrove sediments might weaken the microbial metabolisms that enable the mangrove ecosystems to act as a buffer zone for terrestrial nutrients deposition, and induce bioremediation processes accompanied with an increase in greenhouse gas emission.
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Affiliation(s)
- Yingdong Li
- Division of Life Science, The Hong Kong University of Science and Technology, Kowloon, China
| | - Liping Zheng
- CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Yue Zhang
- CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Hongbin Liu
- Division of Life Science, The Hong Kong University of Science and Technology, Kowloon, China.
| | - Hongmei Jing
- CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.
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McAllister SM, Moore RM, Gartman A, Luther GW, Emerson D, Chan CS. The Fe(II)-oxidizing Zetaproteobacteria: historical, ecological and genomic perspectives. FEMS Microbiol Ecol 2019; 95:fiz015. [PMID: 30715272 PMCID: PMC6443915 DOI: 10.1093/femsec/fiz015] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 01/29/2019] [Indexed: 01/22/2023] Open
Abstract
The Zetaproteobacteria are a class of bacteria typically associated with marine Fe(II)-oxidizing environments. First discovered in the hydrothermal vents at Loihi Seamount, Hawaii, they have become model organisms for marine microbial Fe(II) oxidation. In addition to deep sea and shallow hydrothermal vents, Zetaproteobacteria are found in coastal sediments, other marine subsurface environments, steel corrosion biofilms and saline terrestrial springs. Isolates from a range of environments all grow by autotrophic Fe(II) oxidation. Their success lies partly in their microaerophily, which enables them to compete with abiotic Fe(II) oxidation at Fe(II)-rich oxic/anoxic transition zones. To determine the known diversity of the Zetaproteobacteria, we have used 16S rRNA gene sequences to define 59 operational taxonomic units (OTUs), at 97% similarity. While some Zetaproteobacteria taxa appear to be cosmopolitan, others are enriched by specific habitats. OTU networks show that certain Zetaproteobacteria co-exist, sharing compatible niches. These niches may correspond with adaptations to O2, H2 and nitrate availability, based on genomic analyses of metabolic potential. Also, a putative Fe(II) oxidation gene has been found in diverse Zetaproteobacteria taxa, suggesting that the Zetaproteobacteria evolved as Fe(II) oxidation specialists. In all, studies suggest that Zetaproteobacteria are widespread, and therefore may have a broad influence on marine and saline terrestrial Fe cycling.
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Affiliation(s)
- Sean M McAllister
- School of Marine Science and Policy, University of Delaware, 700 Pilottown Road, 204 Cannon Lab, Lewes, Delaware, USA 19958
| | - Ryan M Moore
- Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, 205 Delaware Biotechnology Institute, Newark, Delaware, USA 19711
| | - Amy Gartman
- School of Marine Science and Policy, University of Delaware, 700 Pilottown Road, 204 Cannon Lab, Lewes, Delaware, USA 19958
| | - George W Luther
- School of Marine Science and Policy, University of Delaware, 700 Pilottown Road, 204 Cannon Lab, Lewes, Delaware, USA 19958
| | - David Emerson
- Bigelow Laboratory for Ocean Sciences, 60 Bigelow Drive, East Boothbay, Maine, USA 04544
| | - Clara S Chan
- School of Marine Science and Policy, University of Delaware, 700 Pilottown Road, 204 Cannon Lab, Lewes, Delaware, USA 19958
- Department of Geological Sciences, University of Delaware, 101 Penny Hall, Newark, Delaware, USA 19716
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Wu S, Li R, Xie S, Shi C. Depth-related change of sulfate-reducing bacteria community in mangrove sediments: The influence of heavy metal contamination. MARINE POLLUTION BULLETIN 2019; 140:443-450. [PMID: 30803665 DOI: 10.1016/j.marpolbul.2019.01.042] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 01/13/2019] [Accepted: 01/21/2019] [Indexed: 06/09/2023]
Abstract
This study provides new insight towards the effects of heavy metal contamination on sulfate-reducing bacteria (SRB) in mangrove ecosystem. We investigated SRB communities in mangrove sediments (0-30 cm depth) from Futian, Xixiang and Shajing mangrove wetlands in Shenzhen, China, with different heavy metal contamination levels. The results showed that SRB community abundance (1.71 × 107-3.04 × 108 dsrB gene copies g-1 wet weight sediment) was depth-related and significantly correlated with Cd and Ni concentrations. The α-diversity indices of SRB community (Chao1 = 21.25-84.50, Shannon = 2.31-2.96) were significantly correlated with Cd level in mangrove sediments. Desulfobacteraceae, Desulfobulbaceae and Syntrophobacteraceae acted as major SRB groups in mangrove sediments, and Syntrophobacteraceae was most sensitive to metal contamination. UniFrace clustering analysis revealed that SRB community structure was influenced by the heavy metal concentrations. Moreover, redundancy analysis indicated that Cd and total phosphorus were the major environmental factors affecting the SRB structure in mangrove sediments.
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Affiliation(s)
- Sijie Wu
- School of Environment and Energy, Shenzhen Graduate School of Peking University, Shenzhen 518055, Guangdong, China.
| | - Ruili Li
- School of Environment and Energy, Shenzhen Graduate School of Peking University, Shenzhen 518055, Guangdong, China.
| | - Shuguang Xie
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Cong Shi
- School of Environment and Energy, Shenzhen Graduate School of Peking University, Shenzhen 518055, Guangdong, China
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Moitinho MA, Bononi L, Souza DT, Melo IS, Taketani RG. Bacterial Succession Decreases Network Complexity During Plant Material Decomposition in Mangroves. MICROBIAL ECOLOGY 2018; 76:954-963. [PMID: 29687224 DOI: 10.1007/s00248-018-1190-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 04/10/2018] [Indexed: 06/08/2023]
Abstract
In this study, 16S rRNA gene amplicon sequencing was used to assess bacterial diversity and dynamics throughout different stages of leaves decomposition of three plant species (Rhizophora mangle, Laguncularia racemosa, and Avicennia schaueriana) in three distinct mangroves of São Paulo state, Brazil. The experiments were conducted in microcosms. Phylogenetic diversity (Faiths' PD) index showed differences between samples and suggested that some treatments like R. mangle increased their bacterial diversity through time. Principal coordinate analysis revealed that community's profile varied based on mangroves, followed by plant species and time. A clear succession patterns was observed in this study, i.e., some microorganisms with low abundance in the initial phases gradually became dominant (e.g., Alphaproteobacteria), whereas microbes that were initially predominant became low (e.g., Gammaproteobacteria). Co-occurrence analyses were performed for all times of plant degradation aiming to better understand the relationships between bacterial populations. The c-score index was done to test the randomness of the community assemblage during the stages of decomposition. For all degradation time points, the values of the observed c-score were higher than the values of the simulated c-score. This result indicated that during plant decomposition, the bacterial communities presented less co-occurrence than expected by chance and that these communities were not randomly assembled but instead they are driven by species interactions. Network analyses results showed that in the conditions presented in this experiment, the initial stages of leaf decomposition formed more connected and complex networks than the later stages. These results suggest that resource competition was a determinant in these specific mangroves during plant degradation, mainly in the initial periods.
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Affiliation(s)
- Marta A Moitinho
- Laboratory of Environmental Microbiology, Brazilian Agricultural Research Corporation, EMBRAPA Environment, SP 340 Highway-Km 127.5, Jaguariuna, SP, 13820-000, Brazil
- College of Agriculture "Luiz de Queiroz", University of São Paulo, Pádua Dias Avenue, 11, Piracicaba, SP, 13418-900, Brazil
| | - Laura Bononi
- Laboratory of Environmental Microbiology, Brazilian Agricultural Research Corporation, EMBRAPA Environment, SP 340 Highway-Km 127.5, Jaguariuna, SP, 13820-000, Brazil
- College of Agriculture "Luiz de Queiroz", University of São Paulo, Pádua Dias Avenue, 11, Piracicaba, SP, 13418-900, Brazil
| | - Danilo T Souza
- Laboratory of Environmental Microbiology, Brazilian Agricultural Research Corporation, EMBRAPA Environment, SP 340 Highway-Km 127.5, Jaguariuna, SP, 13820-000, Brazil
| | - Itamar S Melo
- Laboratory of Environmental Microbiology, Brazilian Agricultural Research Corporation, EMBRAPA Environment, SP 340 Highway-Km 127.5, Jaguariuna, SP, 13820-000, Brazil
| | - Rodrigo G Taketani
- Laboratory of Environmental Microbiology, Brazilian Agricultural Research Corporation, EMBRAPA Environment, SP 340 Highway-Km 127.5, Jaguariuna, SP, 13820-000, Brazil.
- College of Agriculture "Luiz de Queiroz", University of São Paulo, Pádua Dias Avenue, 11, Piracicaba, SP, 13418-900, Brazil.
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Taketani RG, Moitinho MA, Mauchline TH, Melo IS. Co-occurrence patterns of litter decomposing communities in mangroves indicate a robust community resistant to disturbances. PeerJ 2018; 6:e5710. [PMID: 30310750 PMCID: PMC6174875 DOI: 10.7717/peerj.5710] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 09/08/2018] [Indexed: 12/31/2022] Open
Abstract
Background Mangroves are important coastal ecosystems known for high photosynthetic productivity and the ability to support marine food chains through supply of dissolved carbon or particular organic matter. Most of the carbon found in mangroves is produced by its vegetation and is decomposed in root associated sediment. This process involves a tight interaction between microbial populations, litter chemical composition, and environmental parameters. Here, we study the complex interactions found during litter decomposition in mangroves by applying network analysis to metagenomic data. Methods Leaves of three species of mangrove trees typically found in the southeast of Brazil (Rhizophora mangle, Laguncularia racemosa, and Avicennia schaueriana) were collected in separate litter bags and left on three different mangroves for 60 days. These leaves were subsequently used for metagenome sequencing using Ion Torrent technology. Sequences were annotated in MG-RAST and used for network construction using MENAp. Results The most common phyla were Proteobacteria (classes Gamma and Alphaproteobacteria) followed by Firmicutes (Clostridia and Bacilli). The most abundant protein clusters were associated with the metabolism of carbohydrates, amino acids, and proteins. Non-metric multidimensional scaling of the metagenomic data indicated that substrate (i.e., tree species) did not significantly select for a specific community. Both networks exhibited scale-free characteristics and small world structure due to the low mean shortest path length and high average clustering coefficient. These networks also had a low number of hub nodes most of which were module hubs. Discussion This study demonstrates that under different environmental pressures (i.e., plant species or mangrove location) the microbial community associated with the decaying material forms a robust and stable network.
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Affiliation(s)
- Rodrigo G Taketani
- Department of Soil Sciences, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, SP, Brazil.,Laboratory of Environmental Microbiology, Embrapa Environment, Brazilian Agricultural Research Corporation-EMBRAPA, Jaguariuna, SP, Brazil
| | - Marta A Moitinho
- Laboratory of Environmental Microbiology, Embrapa Environment, Brazilian Agricultural Research Corporation-EMBRAPA, Jaguariuna, SP, Brazil
| | - Tim H Mauchline
- Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, United Kingdom
| | - Itamar S Melo
- Laboratory of Environmental Microbiology, Embrapa Environment, Brazilian Agricultural Research Corporation-EMBRAPA, Jaguariuna, SP, Brazil
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Priya G, Lau NS, Furusawa G, Dinesh B, Foong SY, Amirul AAA. Metagenomic insights into the phylogenetic and functional profiles of soil microbiome from a managed mangrove in Malaysia. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.aggene.2018.07.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Tiralerdpanich P, Sonthiphand P, Luepromchai E, Pinyakong O, Pokethitiyook P. Potential microbial consortium involved in the biodegradation of diesel, hexadecane and phenanthrene in mangrove sediment explored by metagenomics analysis. MARINE POLLUTION BULLETIN 2018; 133:595-605. [PMID: 30041354 DOI: 10.1016/j.marpolbul.2018.06.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 05/22/2018] [Accepted: 06/05/2018] [Indexed: 06/08/2023]
Abstract
Hydrocarbon contamination is a serious problem that degrades the quality of mangrove ecosystems, and bioremediation using autochthonous bacteria is a promising technology to recover an impacted environment. This research investigates the biodegradation rates of diesel, hexadecane and phenanthrene, by conducting a microcosm study and survey of the autochthonous microbial community in contaminated mangrove sediment, using an Illumina MiSeq platform. The biodegradation rates of diesel, hexadecane and phenanthrene were 82, 86 and 8 mg kg-1 sediment day-1, respectively. The removal efficiencies of hexadecane and phenanthrene were >99%, whereas the removal efficiency of diesel was 88%. A 16S rRNA gene amplicon sequence analysis revealed that the major bacterial assemblages detected were Gammaproteobacteria, Deltaproteobacteria, Alphaproteobacteria. The bacterial compositions were relatively constant, while reductions of the supplemented hydrocarbons were observed. The results imply that the autochthonous microorganisms in the mangrove sediment were responsible for the degradation of the respective hydrocarbons. Diesel-, hexadecane- and phenanthrene-degrading bacteria, namely Bacillus sp., Pseudomonas sp., Acinetobacter sp. and Staphylococcus sp., were also isolated from the mangrove sediment. The mangrove sediment provides a potential resource of effective hydrocarbon-degrading bacteria that can be used as an inoculum or further developed as a ready-to-use microbial consortium for the purpose of bioremediation.
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Affiliation(s)
- Parichaya Tiralerdpanich
- International Postgraduate Program in Hazardous Substance and Environmental Management, Chulalongkorn University, 9th Floor, CU Research Building, Phayathai Road, Bangkok 10330, Thailand; Center of Excellence on Hazardous Substance Management, Chulalongkorn University, 8th Floor, CU Research Building, Phayathai Road, Bangkok 10330, Thailand
| | - Prinpida Sonthiphand
- Department of Biology, Faculty of Science, Mahidol University, 272 Rama VI Road, Ratchathewi, Bangkok 10400, Thailand.
| | - Ekawan Luepromchai
- Microbial Technology for Marine Pollution Treatment Research Unit, Department of Microbiology, Faculty of Science, Chulalongkorn University, Phayathai Road, Bangkok 10330, Thailand; Center of Excellence on Hazardous Substance Management, Chulalongkorn University, 8th Floor, CU Research Building, Phayathai Road, Bangkok 10330, Thailand
| | - Onruthai Pinyakong
- Microbial Technology for Marine Pollution Treatment Research Unit, Department of Microbiology, Faculty of Science, Chulalongkorn University, Phayathai Road, Bangkok 10330, Thailand; Center of Excellence on Hazardous Substance Management, Chulalongkorn University, 8th Floor, CU Research Building, Phayathai Road, Bangkok 10330, Thailand
| | - Prayad Pokethitiyook
- Department of Biology, Faculty of Science, Mahidol University, 272 Rama VI Road, Ratchathewi, Bangkok 10400, Thailand
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Puentes-Téllez PE, Falcao Salles J. Construction of Effective Minimal Active Microbial Consortia for Lignocellulose Degradation. MICROBIAL ECOLOGY 2018; 76:419-429. [PMID: 29392382 PMCID: PMC6061470 DOI: 10.1007/s00248-017-1141-5] [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: 10/05/2017] [Accepted: 12/29/2017] [Indexed: 06/02/2023]
Abstract
Enriched microbial communities, obtained from environmental samples through selective processes, can effectively contribute to lignocellulose degradation. Unfortunately, fully controlled industrial degradation processes are difficult to reach given the intrinsically dynamic nature and complexity of the microbial communities, composed of a large number of culturable and unculturable species. The use of less complex but equally effective microbial consortia could improve their applications by allowing for more controlled industrial processes. Here, we combined ecological theory and enrichment principles to develop an effective lignocellulose-degrading minimal active microbial Consortia (MAMC). Following an enrichment of soil bacteria capable of degrading lignocellulose material from sugarcane origin, we applied a reductive-screening approach based on molecular phenotyping, identification, and metabolic characterization to obtain a selection of 18 lignocellulose-degrading strains representing four metabolic functional groups. We then generated 65 compositional replicates of MAMC containing five species each, which vary in the number of functional groups, metabolic potential, and degradation capacity. The characterization of the MAMC according to their degradation capacities and functional diversity measurements revealed that functional diversity positively correlated with the degradation of the most complex lignocellulosic fraction (lignin), indicating the importance of metabolic complementarity, whereas cellulose and hemicellulose degradation were either negatively or not affected by functional diversity. The screening method described here successfully led to the selection of effective MAMC, whose degradation potential reached up 96.5% of the degradation rates when all 18 species were present. A total of seven assembled synthetic communities were identified as the most effective MAMC. A consortium containing Stenotrophomonas maltophilia, Paenibacillus sp., Microbacterium sp., Chryseobacterium taiwanense, and Brevundimonas sp. was found to be the most effective degrading synthetic community.
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Affiliation(s)
- Pilar Eliana Puentes-Téllez
- Microbial Community Ecology, GELIFES - Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
- Department of Biology, Institute of Environmental Biology, Ecology and Biodiversity Group, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Joana Falcao Salles
- Microbial Community Ecology, GELIFES - Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
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Wang HL, Zhang J, Sun QL, Lian C, Sun L. A comparative study revealed first insights into the diversity and metabolisms of the microbial communities in the sediments of Pacmanus and Desmos hydrothermal fields. PLoS One 2017; 12:e0181048. [PMID: 28704556 PMCID: PMC5507547 DOI: 10.1371/journal.pone.0181048] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Accepted: 06/26/2017] [Indexed: 12/02/2022] Open
Abstract
Currently, little is known about the microbial diversity in the sediments of Pacmanus and Desmos hydrothermal fields in Manus Basin. In this study, Illumina-based sequencing of 16S rRNA gene amplicons and metagenomic analysis were conducted to investigate the microbial populations and metabolic profiles in the sediments from four different regions in Pacmanus and Desmos hydrothermal fields. It was found that Gammaproteobacteria and Thaumarchaeota were the most abundant bacterial and archaeal populations, respectively. The autotrophic prokaryotes in the four communities probably fixed CO2 via four major pathways, i.e. Calvin-Benson-Bassham cycle, reductive acetyl-CoA cycle, rTCA cycle, and 3-hydroxypropionate/4-hydroxybutyrate cycle. Ammonia-oxidizing Thaumarchaeota, nitrifiers, denitrifiers, and sulfur oxidizers belonging to the subgroups of Proteobacteria (e.g., alpha, beta, gamma, and epsilon), Nitrospira, and Nitrospina, and sulfate-reducing Desulfobacterales likely played critical roles in nitrogen and sulfur cycling, in which ammonia, sulfur compounds, and hydrogen could be utilized as potential energy sources. These findings revealed new insights into the operational mechanism of the microbial communities associated with Pacmanus and Desmos hydrothermal fields.
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Affiliation(s)
- Hai-liang Wang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jian Zhang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Qing-lei Sun
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Chao Lian
- Key Laboratory of Marine Geology and Environment, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Li Sun
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- * E-mail:
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22
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Duran R, Cravo-Laureau C. Role of environmental factors and microorganisms in determining the fate of polycyclic aromatic hydrocarbons in the marine environment. FEMS Microbiol Rev 2016; 40:814-830. [PMID: 28201512 PMCID: PMC5091036 DOI: 10.1093/femsre/fuw031] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 12/28/2015] [Accepted: 07/24/2016] [Indexed: 11/14/2022] Open
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are widespread in marine ecosystems and originate from natural sources and anthropogenic activities. PAHs enter the marine environment in two main ways, corresponding to chronic pollution or acute pollution by oil spills. The global PAH fluxes in marine environments are controlled by the microbial degradation and the biological pump, which plays a role in particle settling and in sequestration through bioaccumulation. Due to their low water solubility and hydrophobic nature, PAHs tightly adhere to sediments leading to accumulation in coastal and deep sediments. Microbial assemblages play an important role in determining the fate of PAHs in water and sediments, supporting the functioning of biogeochemical cycles and the microbial loop. This review summarises the knowledge recently acquired in terms of both chronic and acute PAH pollution. The importance of the microbial ecology in PAH-polluted marine ecosystems is highlighted as well as the importance of gaining further in-depth knowledge of the environmental services provided by microorganisms.
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Affiliation(s)
- Robert Duran
- Equipe Environnement et Microbiologie, MELODY group, Université de Pau et des Pays de l'Adour, Pau Cedex, France
| | - Cristiana Cravo-Laureau
- Equipe Environnement et Microbiologie, MELODY group, Université de Pau et des Pays de l'Adour, Pau Cedex, France
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23
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Wu P, Xiong X, Xu Z, Lu C, Cheng H, Lyu X, Zhang J, He W, Deng W, Lyu Y, Lou Q, Hong Y, Fang H. Bacterial Communities in the Rhizospheres of Three Mangrove Tree Species from Beilun Estuary, China. PLoS One 2016; 11:e0164082. [PMID: 27695084 PMCID: PMC5047532 DOI: 10.1371/journal.pone.0164082] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 09/19/2016] [Indexed: 01/28/2023] Open
Abstract
The bacterial communities played important roles in the high productivity mangrove ecosystem. In this study, we investigated the vertical distributions of rhizosphere bacteria from three mangrove species (Bruguiera gymnorrhiza, Kandelia candel and Aegiceras corniculatum) in Beilun Estuary, China using high throughput DNA pyrosequencing of the 16S rRNA gene. Phylogenetic analysis showed that bacterial communities from mangrove rhizosphere sediments were dominated by Proteobacteria (mostly Deltaproteobacteria and Gammaproteobacteria), followed by Chloroflexi, Bacteroidetes, Planctomycetes and Acidobacteria. However, the ANOVA analysis on Shannon and Chao1 indices indicated that bacterial communities among sediments of the three mangrove species varied more strongly than the sampling depths. In addition, the PCA result demonstrated that the bacterial communities could be separated into three groups according to the mangrove species. Moreover, the dominated orders Rhodospirillales, GCA004 and envOPS12 were significantly different among sediments of the three mangrove species. The results of this study provided valuable information about the distribution feature of rhizosphere bacteria from Chinese mangrove plants and shed insights into biogeochemical transformations driven by bacteria in rhizosphere sediments.
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Affiliation(s)
- Peng Wu
- South China Sea Environmental Monitoring Center, State Oceanic Administration, Guangzhou, China
| | - Xiaofei Xiong
- South China Sea Environmental Monitoring Center, State Oceanic Administration, Guangzhou, China
| | - Zhanzhou Xu
- South China Sea Environmental Monitoring Center, State Oceanic Administration, Guangzhou, China
| | - Chuqian Lu
- South China Sea Environmental Monitoring Center, State Oceanic Administration, Guangzhou, China
| | - Hao Cheng
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Xiangli Lyu
- South China Sea Environmental Monitoring Center, State Oceanic Administration, Guangzhou, China
| | - Jinghuai Zhang
- South China Sea Environmental Monitoring Center, State Oceanic Administration, Guangzhou, China
| | - Wei He
- South China Sea Environmental Monitoring Center, State Oceanic Administration, Guangzhou, China
| | - Wei Deng
- South China Sea Environmental Monitoring Center, State Oceanic Administration, Guangzhou, China
| | - Yihua Lyu
- South China Sea Environmental Monitoring Center, State Oceanic Administration, Guangzhou, China
| | - Quansheng Lou
- South China Sea Environmental Monitoring Center, State Oceanic Administration, Guangzhou, China
| | - Yiguo Hong
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- * E-mail: (YH); (HF)
| | - Hongda Fang
- South China Sea Environmental Monitoring Center, State Oceanic Administration, Guangzhou, China
- * E-mail: (YH); (HF)
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24
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de Lima Brossi MJ, Jiménez DJ, Cortes-Tolalpa L, van Elsas JD. Soil-Derived Microbial Consortia Enriched with Different Plant Biomass Reveal Distinct Players Acting in Lignocellulose Degradation. MICROBIAL ECOLOGY 2016; 71:616-27. [PMID: 26487437 PMCID: PMC4788684 DOI: 10.1007/s00248-015-0683-7] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 09/27/2015] [Indexed: 05/09/2023]
Abstract
Here, we investigated how different plant biomass, and-for one substrate-pH, drive the composition of degrader microbial consortia. We bred such consortia from forest soil, incubated along nine aerobic sequential - batch enrichments with wheat straw (WS1, pH 7.2; WS2, pH 9.0), switchgrass (SG, pH 7.2), and corn stover (CS, pH 7.2) as carbon sources. Lignocellulosic compounds (lignin, cellulose and xylan) were best degraded in treatment SG, followed by CS, WS1 and WS2. In terms of composition, the consortia became relatively stable after transfers 4 to 6, as evidenced by PCR-DGGE profiles obtained from each consortium DNA. The final consortia differed by ~40 % (bacteria) and ~60 % (fungi) across treatments. A 'core' community represented by 5/16 (bacteria) and 3/14 (fungi) bands was discerned, next to a variable part. The composition of the final microbial consortia was strongly driven by the substrate, as taxonomically-diverse consortia appeared in the different substrate treatments, but not in the (WS) different pH one. Biodegradative strains affiliated to Sphingobacterium kitahiroshimense, Raoultella terrigena, Pseudomonas putida, Stenotrophomonas rhizophila (bacteria), Coniochaeta ligniaria and Acremonium sp. (fungi) were recovered in at least three treatments, whereas strains affiliated to Delftia tsuruhatensis, Paenibacillus xylanexedens, Sanguibacter inulus and Comamonas jiangduensis were treatment-specific.
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Affiliation(s)
- Maria Julia de Lima Brossi
- Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747AG, Groningen, The Netherlands.
| | - Diego Javier Jiménez
- Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747AG, Groningen, The Netherlands
| | - Larisa Cortes-Tolalpa
- Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747AG, Groningen, The Netherlands
| | - Jan Dirk van Elsas
- Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747AG, Groningen, The Netherlands
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25
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Distinct Habitats Select Particular Bacterial Communities in Mangrove Sediments. Int J Microbiol 2016; 2016:3435809. [PMID: 26989418 PMCID: PMC4773542 DOI: 10.1155/2016/3435809] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 01/09/2016] [Accepted: 01/27/2016] [Indexed: 11/18/2022] Open
Abstract
We investigated the relationship among environmental variables, composition, and structure of bacterial communities in different habitats in a mangrove located nearby to an oil exploitation area, aiming to retrieve the natural pattern of bacterial communities in this ecosystem. The T-RFLP analysis showed a high diversity of bacterial populations and an increase in the bacterial richness from habitats closer to the sea and without vegetation (S1) to habitats covered by Avicennia schaueriana (S2) and Rhizophora mangle (S3). Environmental variables in S1 and S2 were more similar than in S3; however, when comparing the bacterial compositions, S2 and S3 shared more OTUs between them, suggesting that the presence of vegetation is an important factor in shaping these bacterial communities. In silico analyses of the fragments revealed a high diversity of the class Gammaproteobacteria in the 3 sites, although in general they presented quite different bacterial composition, which is probably shaped by the specificities of each habitat. This study shows that microhabitats inside of a mangrove ecosystem harbor diverse and distinct microbiota, reinforcing the need to conserve these ecosystems as a whole.
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26
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Abstract
Mangroves are unique, and endangered, coastal ecosystems that play a vital role in the tropical and subtropical environments. A comprehensive description of the microbial communities in these ecosystems is currently lacking, and additional studies are required to have a complete understanding of the functioning and resilience of mangroves worldwide. In this work, we carried out a metagenomic study by comparing the microbial community of mangrove sediment with the rhizosphere microbiome of Avicennia marina, in northern Red Sea mangroves, along the coast of Saudi Arabia. Our results revealed that rhizosphere samples presented similar profiles at the taxonomic and functional levels and differentiated from the microbiome of bulk soil controls. Overall, samples showed predominance by Proteobacteria, Bacteroidetes and Firmicutes, with high abundance of sulfate reducers and methanogens, although specific groups were selectively enriched in the rhizosphere. Functional analysis showed significant enrichment in 'metabolism of aromatic compounds', 'mobile genetic elements', 'potassium metabolism' and 'pathways that utilize osmolytes' in the rhizosphere microbiomes. To our knowledge, this is the first metagenomic study on the microbiome of mangroves in the Red Sea, and the first application of unbiased 454-pyrosequencing to study the rhizosphere microbiome associated with A. marina. Our results provide the first insights into the range of functions and microbial diversity in the rhizosphere and soil sediments of gray mangrove (A. marina) in the Red Sea.
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27
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Jing H, Xia X, Liu H, Zhou Z, Wu C, Nagarajan S. Anthropogenic impact on diazotrophic diversity in the mangrove rhizosphere revealed by nifH pyrosequencing. Front Microbiol 2015; 6:1172. [PMID: 26539189 PMCID: PMC4612719 DOI: 10.3389/fmicb.2015.01172] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Accepted: 10/09/2015] [Indexed: 11/13/2022] Open
Abstract
Diazotrophs in the mangrove rhizosphere play a major role in providing new nitrogen to the mangrove ecosystem and their composition and activity are strongly influenced by anthropogenic activity and ecological conditions. In this study, the diversity of the diazotroph communities in the rhizosphere sediment of five tropical mangrove sites with different levels of pollution along the north and south coastline of Singapore were studied by pyrosequencing of the nifH gene. Bioinformatics analysis revealed that in all the studied locations, the diazotroph communities comprised mainly of members of the diazotrophic cluster I and cluster III. The detected cluster III diazotrophs, which were composed entirely of sulfate-reducing bacteria, were more abundant in the less polluted locations. The metabolic capacities of these diazotrophs indicate the potential for bioremediation and resiliency of the ecosystem to anthropogenic impact. In heavily polluted locations, the diazotrophic community structures were markedly different and the diversity of species was significantly reduced when compared with those in a pristine location. This, together with the increased abundance of Marinobacterium, which is a bioindicator of pollution, suggests that anthropogenic activity has a negative impact on the genetic diversity of diazotrophs in the mangrove rhizosphere.
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Affiliation(s)
- Hongmei Jing
- Sanya Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences Sanya, China
| | - Xiaomin Xia
- Division of Life Science, The Hong Kong University of Science and Technology Kowloon, Hong Kong
| | - Hongbin Liu
- Division of Life Science, The Hong Kong University of Science and Technology Kowloon, Hong Kong
| | - Zhi Zhou
- Department of Civil and Environmental Engineering, Faculty of Engineering, National University of Singapore Singapore, Singapore
| | - Chen Wu
- Department of Civil and Environmental Engineering, Faculty of Engineering, National University of Singapore Singapore, Singapore
| | - Sanjay Nagarajan
- Department of Civil and Environmental Engineering, Faculty of Engineering, National University of Singapore Singapore, Singapore
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28
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Stauffert M, Cravo-Laureau C, Duran R. Dynamic of sulphate-reducing microorganisms in petroleum-contaminated marine sediments inhabited by the polychaete Hediste diversicolor. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:15273-15284. [PMID: 25256587 DOI: 10.1007/s11356-014-3624-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 09/16/2014] [Indexed: 06/03/2023]
Abstract
The behaviour of sulphate-reducing microbial community was investigated at the oxic-anoxic interface (0-2 cm) of marine sediments when submitted to oil and enhanced bioturbation activities by the addition of Hediste diversicolor. Although total hydrocarbon removal was not improved by the addition of H. diversicolor, terminal restriction fragment length polymorphism (T-RFLP) analyses based on dsrAB (dissimilatory sulphite reductase) genes and transcripts showed different patterns according to the presence of H. diversicolor which favoured the abundance of dsrB genes during the early stages of incubation. Complementary DNA (cDNA) dsrAB libraries revealed that in presence of H. diversicolor, most dsrAB sequences belonged to hydrocarbonoclastic Desulfobacteraceae, suggesting that sulphate-reducing microorganisms (SRMs) may play an active role in hydrocarbon biodegradation in sediments where the reworking activity is enhanced. Furthermore, the presence of dsrAB sequences related to sequences found associated to environments with high dinitrogen fixation activity suggested potential N2 fixation by SRMs in bioturbated-polluted sediments.
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Affiliation(s)
- Magalie Stauffert
- Equipe Environnement et Microbiologie, Université de Pau et des Pays de l'Adour, IPREM UMR CNRS 5254, BP 1155, 64013, Pau Cedex, France
| | - Cristiana Cravo-Laureau
- Equipe Environnement et Microbiologie, Université de Pau et des Pays de l'Adour, IPREM UMR CNRS 5254, BP 1155, 64013, Pau Cedex, France.
| | - Robert Duran
- Equipe Environnement et Microbiologie, Université de Pau et des Pays de l'Adour, IPREM UMR CNRS 5254, BP 1155, 64013, Pau Cedex, France
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29
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Sanni GO, Coulon F, McGenity TJ. Dynamics and distribution of bacterial and archaeal communities in oil-contaminated temperate coastal mudflat mesocosms. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:15230-15247. [PMID: 25869427 DOI: 10.1007/s11356-015-4313-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 03/02/2015] [Indexed: 06/04/2023]
Abstract
Mudflats are ecologically important habitats that are susceptible to oil pollution, but intervention is difficult in these fine-grained sediments, and so clean-up usually relies on natural attenuation. Therefore, we investigated the impact of crude oil on the bacterial, diatom and archaeal communities within the upper parts of the diatom-dominated sediment and the biofilm that detached from the surface at high tide. Biodegradation of petroleum hydrocarbons was rapid, with a 50 % decrease in concentration in the 0-2-mm section of sediment by 3 days, indicating the presence of a primed hydrocarbon-degrading community. The biggest oil-induced change was in the biofilm that detached from the sediment, with increased relative abundance of several types of diatom and of the obligately hydrocarbonoclastic Oleibacter sp., which constituted 5 % of the pyrosequences in the oiled floating biofilm on day 3 compared to 0.6 % in the non-oiled biofilm. Differences in bacterial community composition between oiled and non-oiled samples from the 0-2-mm section of sediment were only significant at days 12 to 28, and the 2-4-mm-sediment bacterial communities were not significantly affected by oil. However, specific members of the Chromatiales were detected (1 % of sequences in the 2-4-mm section) only in the oiled sediment, supporting other work that implicates them in anaerobic hydrocarbon degradation. Unlike the Bacteria, the archaeal communities were not significantly affected by oil. In fact, changes in community composition over time, perhaps caused by decreased nutrient concentration and changes in grazing pressure, overshadowed the effect of oil for both Bacteria and Archaea. Many obligate hydrocarbonoclastic and generalist oil-degrading bacteria were isolated, and there was little correspondence between the isolates and the main taxa detected by pyrosequencing of sediment-extracted DNA, except for Alcanivorax, Thalassolituus, Cycloclasticus and Roseobacter spp., which were detected by both methods.
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Affiliation(s)
- Gbemisola O Sanni
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Frédéric Coulon
- School of Energy, Environment and Agrifood, Cranfield University, Building 40, Cranfield, Bedfordshire, MK43 0AL, UK
| | - Terry J McGenity
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK.
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30
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Liu J, Liu X, Wang M, Qiao Y, Zheng Y, Zhang XH. Bacterial and archaeal communities in sediments of the north Chinese marginal seas. MICROBIAL ECOLOGY 2015; 70:105-17. [PMID: 25501892 DOI: 10.1007/s00248-014-0553-8] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 12/01/2014] [Indexed: 05/16/2023]
Abstract
Microbial communities of the Chinese marginal seas have rarely been reported. Here, bacterial and archaeal community structures and abundance in the surface sediment of four sea areas including the Bohai Sea (BS), North Yellow Sea (NYS), South Yellow Sea (SYS), and the north East China Sea (NECS) were surveyed by 16S ribosomal RNA (rRNA) gene pyrosequencing and quantitative PCR. The results showed that microbial communities of the four geographic areas were distinct from each other at the operational taxonomic unit (OTU) level, whereas the microbial communities of the BS, NYS, and SYS were more similar to each other than to the NECS at higher taxonomic levels. Across all samples, Bacteria were numerically dominant relative to Archaea, and among them, Gammaproteobacteria and Euryarchaeota were predominant in the BS, NYS, and SYS, while Deltaproteobacteria and Thaumarchaeota were prevalent in the NECS. The most abundant bacterial genera were putative sulfur oxidizer and sulfate reducer, suggesting that sulfur cycle processes might prevail in these areas, and the high abundance of dsrB (10(7)-10(8) copies g(-1)) in all sites verified the dominance of sulfate reducer in the north Chinese marginal seas. The differences in sediment sources among the sampling areas were potential explanations for the observed microbial community variations. Furthermore, temperature and dissolved oxygen of bottom water were significant environmental factors in determining both bacterial and archaeal communities, whereas chlorophyll a in sediment was significant only in structuring archaeal community. This study presented an outline of benthic microbial communities and provided insights into understanding the biogeochemical cycles in sediments of the north Chinese marginal seas.
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Affiliation(s)
- Jiwen Liu
- College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, 266003, Qingdao, China
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31
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Basak P, Majumder NS, Nag S, Bhattacharyya A, Roy D, Chakraborty A, SenGupta S, Roy A, Mukherjee A, Pattanayak R, Ghosh A, Chattopadhyay D, Bhattacharyya M. Spatiotemporal analysis of bacterial diversity in sediments of Sundarbans using parallel 16S rRNA gene tag sequencing. MICROBIAL ECOLOGY 2015; 69:500-511. [PMID: 25256302 DOI: 10.1007/s00248-014-0498-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 09/10/2014] [Indexed: 06/03/2023]
Abstract
The influence of temporal and spatial variations on the microbial community composition was assessed in the unique coastal mangrove of Sundarbans using parallel 16S rRNA gene pyrosequencing. The total sediment DNA was extracted and subjected to the 16S rRNA gene pyrosequencing, which resulted in 117 Mbp of data from three experimental stations. The taxonomic analysis of the pyrosequencing data was grouped into 24 different phyla. In general, Proteobacteria were the most dominant phyla with predominance of Deltaproteobacteria, Alphaproteobacteria, and Gammaproteobacteria within the sediments. Besides Proteobacteria, there are a number of sequences affiliated to the following major phyla detected in all three stations in both the sampling seasons: Actinobacteria, Bacteroidetes, Planctomycetes, Acidobacteria, Chloroflexi, Cyanobacteria, Nitrospira, and Firmicutes. Further taxonomic analysis revealed abundance of micro-aerophilic and anaerobic microbial population in the surface layers, suggesting anaerobic nature of the sediments in Sundarbans. The results of this study add valuable information about the composition of microbial communities in Sundarbans mangrove and shed light on possible transformations promoted by bacterial communities in the sediments.
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Affiliation(s)
- Pijush Basak
- Department of Biochemistry, University College of Science, University of Calcutta, 35, Ballygunge Circular Road, Calcutta, 700019, India
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32
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Variations of Bacterial Community Structure and Composition in Mangrove Sediment at Different Depths in Southeastern Brazil. DIVERSITY-BASEL 2014. [DOI: 10.3390/d6040827] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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33
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Yang L, Kent AD, Wang X, Funk TL, Gates RS, Zhang Y. Moisture effects on gas-phase biofilter ammonia removal efficiency, nitrous oxide generation, and microbial communities. JOURNAL OF HAZARDOUS MATERIALS 2014; 271:292-301. [PMID: 24641992 DOI: 10.1016/j.jhazmat.2014.01.058] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 01/23/2014] [Accepted: 01/25/2014] [Indexed: 06/03/2023]
Abstract
We established a four-biofilter setup to examine the effects of moisture content (MC) on biofilter performance, including NH3 removal and N2O generation. We hypothesized that MC increase can improve NH3 removal, stimulate N2O generation and alter the composition and function of microbial communities. We found that NH3 removal efficiency was greatly improved when MC increased from 35 to 55%, but further increasing MC to 63% did not help much; while N2O concentration was low at 35-55% MC, but dramatically increased at 63% MC. Decreasing MC from 63 to 55% restored N2O concentration. Examination of amoA communities using T-RFLP and real-time qPCR showed that the composition and abundance of ammonia oxidizers were not significantly changed in a "moisture disturbance-disturbance relief" process in which MC was increased from 55 to 63% and then reduced to 55%. This observation supported the changes of NH3 removal efficiency. The composition of nosZ community was altered at 63% MC and then was recovered at 55% MC, which indicates resilience to moisture disturbance. The abundance of nosZ community was negatively correlated with moisture content in this process, and the decreased nosZ abundance at 63% MC explained the observation of increased N2O concentration at that condition.
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Affiliation(s)
- Liangcheng Yang
- Department of Agricultural and Biological Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Angela D Kent
- Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Xinlei Wang
- Department of Agricultural and Biological Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Ted L Funk
- Department of Agricultural and Biological Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Richard S Gates
- Department of Agricultural and Biological Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Yuanhui Zhang
- Department of Agricultural and Biological Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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34
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Scott NM, Hess M, Bouskill NJ, Mason OU, Jansson JK, Gilbert JA. The microbial nitrogen cycling potential is impacted by polyaromatic hydrocarbon pollution of marine sediments. Front Microbiol 2014; 5:108. [PMID: 24723913 PMCID: PMC3971162 DOI: 10.3389/fmicb.2014.00108] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Accepted: 03/03/2014] [Indexed: 11/20/2022] Open
Abstract
During hydrocarbon exposure, the composition and functional dynamics of marine microbial communities are altered, favoring bacteria that can utilize this rich carbon source. Initial exposure of high levels of hydrocarbons in aerobic surface sediments can enrich growth of heterotrophic microorganisms having hydrocarbon degradation capacity. As a result, there can be a localized reduction in oxygen potential within the surface layer of marine sediments causing anaerobic zones. We hypothesized that increasing exposure to elevated hydrocarbon concentrations would positively correlate with an increase in denitrification processes and the net accumulation of dinitrogen. This hypothesis was tested by comparing the relative abundance of genes associated with nitrogen metabolism and nitrogen cycling identified in 6 metagenomes from sediments contaminated by polyaromatic hydrocarbons from the Deepwater Horizon (DWH) oil spill in the Gulf of Mexico, and 3 metagenomes from sediments associated with natural oil seeps in the Santa Barbara Channel. An additional 8 metagenomes from uncontaminated sediments from the Gulf of Mexico were analyzed for comparison. We predicted relative changes in metabolite turnover as a function of the differential microbial gene abundances, which showed predicted accumulation of metabolites associated with denitrification processes, including anammox, in the contaminated samples compared to uncontaminated sediments, with the magnitude of this change being positively correlated to the hydrocarbon concentration and exposure duration. These data highlight the potential impact of hydrocarbon inputs on N cycling processes in marine sediments and provide information relevant for system scale models of nitrogen metabolism in affected ecosystems.
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Affiliation(s)
- Nicole M Scott
- Institute of Genomic and Systems Biology, Argonne National Laboratory Lemont, IL, USA ; Department of Ecology and Evolutionary Biology, University of Chicago Chicago, IL, USA
| | - Matthias Hess
- Energy and Efficiency Division, Chemical and Biological Process Development Group, Pacific Northwest National Laboratory Richland, WA, USA ; Systems Microbiology and Biotechnology Group, Washington State University Richland, WA, USA
| | - Nick J Bouskill
- Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Olivia U Mason
- Earth, Ocean and Atmospheric Science, Florida State University Tallahassee, FL, USA
| | - Janet K Jansson
- Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Jack A Gilbert
- Institute of Genomic and Systems Biology, Argonne National Laboratory Lemont, IL, USA ; Department of Ecology and Evolutionary Biology, University of Chicago Chicago, IL, USA
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35
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Cravo-Laureau C, Duran R. Marine coastal sediments microbial hydrocarbon degradation processes: contribution of experimental ecology in the omics'era. Front Microbiol 2014; 5:39. [PMID: 24575083 PMCID: PMC3921567 DOI: 10.3389/fmicb.2014.00039] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 01/21/2014] [Indexed: 11/18/2022] Open
Abstract
Coastal marine sediments, where important biological processes take place, supply essential ecosystem services. By their location, such ecosystems are particularly exposed to human activities as evidenced by the recent Deepwater Horizon disaster. This catastrophe revealed the importance to better understand the microbial processes involved on hydrocarbon degradation in marine sediments raising strong interests of the scientific community. During the last decade, several studies have shown the key role played by microorganisms in determining the fate of hydrocarbons in oil-polluted sediments but only few have taken into consideration the whole sediment’s complexity. Marine coastal sediment ecosystems are characterized by remarkable heterogeneity, owning high biodiversity and are subjected to fluctuations in environmental conditions, especially to important oxygen oscillations due to tides. Thus, for understanding the fate of hydrocarbons in such environments, it is crucial to study microbial activities, taking into account sediment characteristics, physical-chemical factors (electron acceptors, temperature), nutrients, co-metabolites availability as well as sediment’s reworking due to bioturbation activities. Key information could be collected from in situ studies, which provide an overview of microbial processes, but it is difficult to integrate all parameters involved. Microcosm experiments allow to dissect in-depth some mechanisms involved in hydrocarbon degradation but exclude environmental complexity. To overcome these lacks, strategies have been developed, by creating experiments as close as possible to environmental conditions, for studying natural microbial communities subjected to oil pollution. We present here a review of these approaches, their results and limitation, as well as the promising future of applying “omics” approaches to characterize in-depth microbial communities and metabolic networks involved in hydrocarbon degradation. In addition, we present the main conclusions of our studies in this field.
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Affiliation(s)
- Cristiana Cravo-Laureau
- Equipe Environnement et Microbiologie UMR IPREM 5254, Université de Pau et des Pays de l'Adour Pau, France
| | - Robert Duran
- Equipe Environnement et Microbiologie UMR IPREM 5254, Université de Pau et des Pays de l'Adour Pau, France
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Stauffert M, Duran R, Gassie C, Cravo-Laureau C. Response of archaeal communities to oil spill in bioturbated mudflat sediments. MICROBIAL ECOLOGY 2014; 67:108-119. [PMID: 24057322 DOI: 10.1007/s00248-013-0288-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 09/03/2013] [Indexed: 06/02/2023]
Abstract
The response of archaeal community to oil spill with the combined effect of the bioturbation activity of the polychaetes Hediste diversicolor was determined in mudflat sediments from the Aber-Benoît basin (Brittany, French Atlantic coast), maintained in microcosms. The dynamics of the archaeal community was monitored by combining comparative terminal restriction fragment length polymorphism (T-RFLP) fingerprints and sequence library analyses based on 16S rRNA genes and 16S cDNA. Methanogens were also followed by targeting the mcrA gene. Crenarchaeota were always detected in all communities irrespective of the addition of H. diversicolor and/or oil. In the presence of oil, modifications of archaeal community structures were observed. These modifications were more pronounced when H. diversicolor was added resulting in a more diverse community especially for the Euryarchaeota and Thaumarchaeota. The analysis of mcrA transcripts showed a specific structure for each condition since the beginning of the experiment. Overall, oiled microcosms showed different communities irrespective of H. diversicolor addition, while similar hydrocarbon removal capacities were observed.
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Affiliation(s)
- Magalie Stauffert
- Equipe Environnement et Microbiologie, IPREM - UMR CNRS 5254, Université de Pau et des Pays de l'Adour, BP 1155, 64013, Pau Cedex, France
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Simarro R, González N, Bautista LF, Molina MC. Assessment of the efficiency of in situ bioremediation techniques in a creosote polluted soil: change in bacterial community. JOURNAL OF HAZARDOUS MATERIALS 2013; 262:158-167. [PMID: 24025312 DOI: 10.1016/j.jhazmat.2013.08.025] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Revised: 07/29/2013] [Accepted: 08/11/2013] [Indexed: 06/02/2023]
Abstract
This work aimed to assess the effectiveness of different in situ bioremediation treatments (bioaugmentation, biostimulation, bioaugmentation and biostimulation, and natural attenuation) on creosote polluted soil. Toxicity, microbial respiration, creosote degradation and the evolution of bacterial communities were analyzed. Results showed that creosote decreased significantly in all treatments, and no significant differences were found between treatments. However, some specific polycyclic aromatic hydrocarbons (PAH) were degraded to a greater extent by biostimulation. The dominance of low temperatures (8.9 °C average) slowed down microbial creosote and PAH uptake and, despite significantly creosote degradation (>60%) at the end of the experiment, toxicity remained constant and high throughout the biodegradation process. DGGE results revealed that biostimulation showed the highest microbial biodiversity, although at the end of the biodegradation process, community composition in all treatments was different from that of the control assay (unpolluted soil). The active uncultured bacteria belonged to the genera Pseudomonas, Sphingomonas, Flexibacter, Pantoea and Balneimonas, the latter two of which have not been previously described as PAH degraders. The majority of the species identified during the creosote biodegradation belonged to Pseudomonas genus, which has been widely studied in bioremediation processes. Results confirmed that some bacteria have an intrinsic capacity to degrade the creosote without previous exposure.
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Affiliation(s)
- R Simarro
- Department of Biology and Geology, ESCET, Universidad Rey Juan Carlos, E-28933 Móstoles, Madrid, Spain
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Thompson C, Beys-da-Silva W, Santi L, Berger M, Vainstein M, Guima rães J, Vasconcelos AT. A potential source for cellulolytic enzyme discovery and environmental aspects revealed through metagenomics of Brazilian mangroves. AMB Express 2013; 3:65. [PMID: 24160319 PMCID: PMC3922913 DOI: 10.1186/2191-0855-3-65] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 10/21/2013] [Indexed: 11/19/2022] Open
Abstract
The mangroves are among the most productive and biologically important environments. The possible presence of cellulolytic enzymes and microorganisms useful for biomass degradation as well as taxonomic and functional aspects of two Brazilian mangroves were evaluated using cultivation and metagenomic approaches. From a total of 296 microorganisms with visual differences in colony morphology and growth (including bacteria, yeast and filamentous fungus), 179 (60.5%) and 117 (39.5%) were isolated from the Rio de Janeiro (RJ) and Bahia (BA) samples, respectively. RJ metagenome showed the higher number of microbial isolates, which is consistent with its most conserved state and higher diversity. The metagenomic sequencing data showed similar predominant bacterial phyla in the BA and RJ mangroves with an abundance of Proteobacteria (57.8% and 44.6%), Firmicutes (11% and 12.3%) and Actinobacteria (8.4% and 7.5%). A higher number of enzymes involved in the degradation of polycyclic aromatic compounds were found in the BA mangrove. Specific sequences involved in the cellulolytic degradation, belonging to cellulases, hemicellulases, carbohydrate binding domains, dockerins and cohesins were identified, and it was possible to isolate cultivable fungi and bacteria related to biomass decomposition and with potential applications for the production of biofuels. These results showed that the mangroves possess all fundamental molecular tools required for building the cellulosome, which is required for the efficient degradation of cellulose material and sugar release.
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Varon-Lopez M, Dias ACF, Fasanella CC, Durrer A, Melo IS, Kuramae EE, Andreote FD. Sulphur-oxidizing and sulphate-reducing communities in Brazilian mangrove sediments. Environ Microbiol 2013; 16:845-55. [DOI: 10.1111/1462-2920.12237] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Accepted: 07/20/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Maryeimy Varon-Lopez
- Department of Soil Science; ‘Luiz de Queiroz’ College of Agriculture; University of São Paulo; Piracicaba SP Brazil
- Department of Microbial Ecology; Netherlands Institute of Ecology (NIOO/KNAW); Wageningen The Netherlands
| | | | - Cristiane Cipolla Fasanella
- Department of Soil Science; ‘Luiz de Queiroz’ College of Agriculture; University of São Paulo; Piracicaba SP Brazil
| | - Ademir Durrer
- Department of Soil Science; ‘Luiz de Queiroz’ College of Agriculture; University of São Paulo; Piracicaba SP Brazil
| | - Itamar Soares Melo
- Laboratory of Environmental Microbiology; Embrapa Environment; Jaguariúna SP Brazil
| | - Eiko Eurya Kuramae
- Department of Microbial Ecology; Netherlands Institute of Ecology (NIOO/KNAW); Wageningen The Netherlands
| | - Fernando Dini Andreote
- Department of Soil Science; ‘Luiz de Queiroz’ College of Agriculture; University of São Paulo; Piracicaba SP Brazil
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Biodegradation of aged diesel in diverse soil matrixes: impact of environmental conditions and bioavailability on microbial remediation capacity. Biodegradation 2012; 24:487-98. [DOI: 10.1007/s10532-012-9605-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Accepted: 11/09/2012] [Indexed: 10/27/2022]
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Simarro R, González N, Bautista LF, Molina MC. Biodegradation of high-molecular-weight polycyclic aromatic hydrocarbons by a wood-degrading consortium at low temperatures. FEMS Microbiol Ecol 2012; 83:438-49. [DOI: 10.1111/1574-6941.12006] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2011] [Revised: 08/28/2012] [Accepted: 09/02/2012] [Indexed: 11/27/2022] Open
Affiliation(s)
- Raquel Simarro
- Department of Biology and Geology; ESCET; Universidad Rey Juan Carlos; Madrid; Spain
| | - Natalia González
- Department of Biology and Geology; ESCET; Universidad Rey Juan Carlos; Madrid; Spain
| | - Luis Fernando Bautista
- Department of Chemical and Environmental Technology; ESCET; Universidad Rey Juan Carlos; Madrid; Spain
| | - Maria Carmen Molina
- Department of Biology and Geology; ESCET; Universidad Rey Juan Carlos; Madrid; Spain
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Ghizelini AM, Mendonça-Hagler LCS, Macrae A. Microbial diversity in Brazilian mangrove sediments - a mini review. Braz J Microbiol 2012; 43:1242-54. [PMID: 24031949 PMCID: PMC3769006 DOI: 10.1590/s1517-83822012000400002] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Accepted: 06/07/2012] [Indexed: 11/21/2022] Open
Abstract
The importance and protection of mangrove ecosystems has been recognized in Brazilian Federal law since 1965. Being protected in law, however, has not always guaranteed their protection in practice. Mangroves are found in coastal and estuarine locations, which are prime real estate for the growth of cities, ports and other economic activities important for Brazilian development. In this mini-review we introduce what mangroves are and why they are so important. We give a brief overview of the microbial diversity found in mangrove sediments and then focus on diversity studies from Brazilian mangroves. We highlight the breadth and depth of knowledge about mangrove microbial communities gained from studying Brazilian mangroves. We report on the exciting findings of molecular microbial ecology methods that have been very successfully applied to study bacterial communities. We note that there have been fewer studies that focus on fungal communities and that fungal diversity studies deserve more attention. The review ends with a look at how a combination of new molecular biology methods and isolation studies are being developed to monitor and conserve mangrove ecosystems and their associated microbial communities. These recent studies are having a global impact and we hope they will help to protect and re-establish mangrove ecosystems.
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Affiliation(s)
- Angela Michelato Ghizelini
- Programa de Pós Graduação em Biotecnologia Vegetal, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, RJ, Brasil
| | | | - Andrew Macrae
- Programa de Pós Graduação em Biotecnologia Vegetal, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, RJ, Brasil
- Instituto de Microbiologia Prof. Paulo de Góes, Universidade Federal do Rio de Janeiro, RJ, Brasil
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Andrade LL, Leite DCA, Ferreira EM, Ferreira LQ, Paula GR, Maguire MJ, Hubert CRJ, Peixoto RS, Domingues RMCP, Rosado AS. Microbial diversity and anaerobic hydrocarbon degradation potential in an oil-contaminated mangrove sediment. BMC Microbiol 2012; 12:186. [PMID: 22935169 PMCID: PMC3579730 DOI: 10.1186/1471-2180-12-186] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2012] [Accepted: 08/23/2012] [Indexed: 12/04/2022] Open
Abstract
Background Mangrove forests are coastal wetlands that provide vital ecosystem services and serve as barriers against natural disasters like tsunamis, hurricanes and tropical storms. Mangroves harbour a large diversity of organisms, including microorganisms with important roles in nutrient cycling and availability. Due to tidal influence, mangroves are sites where crude oil from spills farther away can accumulate. The relationship between mangrove bacterial diversity and oil degradation in mangrove sediments remains poorly understood. Results Mangrove sediment was sampled from 0–5, 15–20 and 35–40 cm depth intervals from the Suruí River mangrove (Rio de Janeiro, Brazil), which has a history of oil contamination. DGGE fingerprinting for bamA, dsr and 16S rRNA encoding fragment genes, and qPCR analysis using dsr and 16S rRNA gene fragment revealed differences with sediment depth. Conclusions Analysis of bacterial 16S rRNA gene diversity revealed changes with depth. DGGE for bamA and dsr genes shows that the anaerobic hydrocarbon-degrading community profile also changed between 5 and 15 cm depth, and is similar in the two deeper sediments, indicating that below 15 cm the anaerobic hydrocarbon-degrading community appears to be well established and homogeneous in this mangrove sediment. qPCR analysis revealed differences with sediment depth, with general bacterial abundance in the top layer (0–5 cm) being greater than in both deeper sediment layers (15–20 and 35–40 cm), which were similar to each other.
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Affiliation(s)
- Luiza L Andrade
- Laboratório de Ecologia Molecular Microbiana, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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Andreote FD, Jiménez DJ, Chaves D, Dias ACF, Luvizotto DM, Dini-Andreote F, Fasanella CC, Lopez MV, Baena S, Taketani RG, de Melo IS. The microbiome of Brazilian mangrove sediments as revealed by metagenomics. PLoS One 2012; 7:e38600. [PMID: 22737213 PMCID: PMC3380894 DOI: 10.1371/journal.pone.0038600] [Citation(s) in RCA: 182] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Accepted: 05/11/2012] [Indexed: 11/25/2022] Open
Abstract
Here we embark in a deep metagenomic survey that revealed the taxonomic and potential metabolic pathways aspects of mangrove sediment microbiology. The extraction of DNA from sediment samples and the direct application of pyrosequencing resulted in approximately 215 Mb of data from four distinct mangrove areas (BrMgv01 to 04) in Brazil. The taxonomic approaches applied revealed the dominance of Deltaproteobacteria and Gammaproteobacteria in the samples. Paired statistical analysis showed higher proportions of specific taxonomic groups in each dataset. The metabolic reconstruction indicated the possible occurrence of processes modulated by the prevailing conditions found in mangrove sediments. In terms of carbon cycling, the sequences indicated the prevalence of genes involved in the metabolism of methane, formaldehyde, and carbon dioxide. With respect to the nitrogen cycle, evidence for sequences associated with dissimilatory reduction of nitrate, nitrogen immobilization, and denitrification was detected. Sequences related to the production of adenylsulfate, sulfite, and H2S were relevant to the sulphur cycle. These data indicate that the microbial core involved in methane, nitrogen, and sulphur metabolism consists mainly of Burkholderiaceae, Planctomycetaceae, Rhodobacteraceae, and Desulfobacteraceae. Comparison of our data to datasets from soil and sea samples resulted in the allotment of the mangrove sediments between those samples. The results of this study add valuable data about the composition of microbial communities in mangroves and also shed light on possible transformations promoted by microbial organisms in mangrove sediments.
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Affiliation(s)
- Fernando Dini Andreote
- Department of Soil Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil.
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Mendes LW, Taketani RG, Navarrete AA, Tsai SM. Shifts in phylogenetic diversity of archaeal communities in mangrove sediments at different sites and depths in southeastern Brazil. Res Microbiol 2012; 163:366-77. [PMID: 22683855 DOI: 10.1016/j.resmic.2012.05.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2011] [Accepted: 05/16/2012] [Indexed: 11/16/2022]
Abstract
This study focused on the structure and composition of archaeal communities in sediments of tropical mangroves in order to obtain sufficient insight into two Brazilian sites from different locations (one pristine and another located in an urban area) and at different depth levels from the surface. Terminal restriction fragment length polymorphism (T-RFLP) of PCR-amplified 16S rRNA gene fragments was used to scan the archaeal community structure, and 16S rRNA gene clone libraries were used to determine the community composition. Redundancy analysis of T-RFLP patterns revealed differences in archaeal community structure according to location, depth and soil attributes. Parameters such as pH, organic matter, potassium and magnesium presented significant correlation with general community structure. Furthermore, phylogenetic analysis revealed a community composition distributed differently according to depth where, in shallow samples, 74.3% of sequences were affiliated with Euryarchaeota and 25.7% were shared between Crenarchaeota and Thaumarchaeota, while for the deeper samples, 24.3% of the sequences were affiliated with Euryarchaeota and 75.7% with Crenarchaeota and Thaumarchaeota. Archaeal diversity measurements based on 16S rRNA gene clone libraries decreased with increasing depth and there was a greater difference between depths (<18% of sequences shared) than sites (>25% of sequences shared). Taken together, our findings indicate that mangrove ecosystems support a diverse archaeal community; it might possibly be involved in nutrient cycles and are affected by sediment properties, depth and distinct locations.
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Affiliation(s)
- Lucas William Mendes
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo, Av Centenario, 303 Piracicaba, SP, CEP 13400-970, Brazil.
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Bruce T, de Castro A, Kruger R, Thompson CC, Thompson FL. Microbial Diversity of Brazilian Biomes. ADVANCES IN MICROBIAL ECOLOGY 2012. [DOI: 10.1007/978-1-4614-2182-5_13] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Diversity and identification of methanogenic archaea and sulphate-reducing bacteria in sediments from a pristine tropical mangrove. Antonie van Leeuwenhoek 2010; 97:401-11. [PMID: 20195901 DOI: 10.1007/s10482-010-9422-8] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2010] [Accepted: 02/09/2010] [Indexed: 10/19/2022]
Abstract
Mangrove sediments are anaerobic ecosystems rich in organic matter. This environment is optimal for anaerobic microorganisms, such as sulphate-reducing bacteria and methanogenic archaea, which are responsible for nutrient cycling. In this study, the diversity of these two functional guilds was evaluated in a pristine mangrove forest using denaturing gradient gel electrophoresis (DGGE) and clone library sequencing in a 50 cm vertical profile sampled every 5.0 cm. DGGE profiles indicated that both groups presented higher richness in shallow samples (0-30 cm) with a steep decrease in richness beyond that depth. According to redundancy analysis, this alteration significantly correlated with a decrease in the amount of organic matter. Clone library sequencing indicated that depth had a strong effect on the selection of dissimilatory sulphate reductase (dsrB) operational taxonomic units (OTUs), as indicated by the small number of shared OTUs found in shallow (0.0 cm) and deep (40.0 cm) libraries. On the other hand, methyl coenzyme-M reductase (mcrA) libraries indicated that most of the OTUs found in the shallow library were present in the deep library. These results show that these two guilds co-exist in these mangrove sediments and indicate important roles for these organisms in nutrient cycling within this ecosystem.
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