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Zhang MZ, Li WT, Liu WJ, Zheng YL. Rhizosphere microbial community construction during the latitudinal spread of the invader Chromolaena odorata. BMC Microbiol 2024; 24:294. [PMID: 39107680 PMCID: PMC11302206 DOI: 10.1186/s12866-024-03450-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 07/30/2024] [Indexed: 08/10/2024] Open
Abstract
The colonization of alien plants in new habitats is typically facilitated by microorganisms present in the soil environment. However, the diversity and structure of the archaeal, bacterial, and fungal communities in the latitudinal spread of alien plants remain unclear. In this study, the rhizosphere and bulk soil of Chromolaena odorata were collected from five latitudes in Pu' er city, Yunnan Province, followed by amplicon sequencing of the soil archaeal, bacterial, and fungal communities. Alpha and beta diversity results revealed that the richness indices and the structures of the archaeal, bacterial, and fungal communities significantly differed along the latitudinal gradient. Additionally, significant differences were observed in the bacterial Shannon index, as well as in the structures of the bacterial and fungal communities between the rhizosphere and bulk soils. Due to the small spatial scale, trends of latitudinal variation in the archaeal, bacterial, and fungal communities were not pronounced. Total potassium, total phosphorus, available nitrogen, available potassium and total nitrogen were the important driving factors affecting the soil microbial community structure. Compared with those in bulk soil, co-occurrence networks in rhizosphere microbial networks presented lower complexity but greater modularity and positive connections. Among the main functional fungi, arbuscular mycorrhizae and soil saprotrophs were more abundant in the bulk soil. The significant differences in the soil microbes between rhizosphere and bulk soils further underscore the impact of C. odorata invasion on soil environments. The significant differences in the soil microbiota along latitudinal gradients, along with specific driving factors, demonstrate distinct nutrient preferences among archaea, bacteria, and fungi and indicate complex microbial responses to soil nutrient elements following the invasion of C. odorata.
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Affiliation(s)
- Ming-Zhu Zhang
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China
| | - Wei-Tao Li
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China.
| | - Wen-Jun Liu
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China
| | - Yu-Long Zheng
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China.
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Mohite JA, Manvi SS, Pardhi K, Bahulikar RA, Deshpande S, Patange S, Joshi M, Kulkarni S, Rahalkar MC. Diverse type I and type II methanotrophs cultivated from an Indian freshwater wetland habitat. Int Microbiol 2024; 27:607-614. [PMID: 37556066 DOI: 10.1007/s10123-023-00415-4] [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: 05/30/2023] [Revised: 07/26/2023] [Accepted: 08/02/2023] [Indexed: 08/10/2023]
Abstract
Wetlands are the main natural sources of methane emissions, which make up a significant portion of greenhouse gas emissions. Such wetland patches serve as rich habitats for aerobic methanotrophs. Limited knowledge of methanotrophs from tropical wetlands widens the scope of study from these habitats. In the present study, a freshwater wetland in a tropical region in India was sampled and serially diluted to obtain methanotrophs in culture. This was followed by the isolation of methanotrophs on agarose-containing plates, incubated under methane: air atmosphere. Methanotrophs are difficult to cultivate, and very few cultures of methanotrophs are available from tropical wetlands. Our current study reports the cultivation of a diverse community of methanotrophs from six genera, namely, Methylomonas, Methylococcus, Methylomagnum, Methylocucumis (type I methanotrophs) along with Methylocystis, Methylosinus (type II methanotrophs). A high abundance of methanotrophs (106-1010 methanotrophs/g fresh weight) was observed in the samples. A Methylococcus strain could represent a putative novel species that was also isolated. Cultures of Methylomagnum and Methylocucumis, two newly described type I methanotrophs exclusively found in rice fields, were obtained. A large number of Methylomonas koyamae strains were cultured. Our study is pioneering in the documentation of culturable methanotrophs from a typical tropical wetland patch. The isolated methanotrophs can act as models for studying methanotroph-based methane mitigation from wetland habitats and can be used for various mitigation and valorization applications.
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Affiliation(s)
- Jyoti A Mohite
- C2-83,84, MACS Agharkar Research Institute, G.G. Agarkar Road, Pune, Maharashtra, 411004, India
- Savitribai Phule Pune University, Ganeshkhind Road, Pune, Maharashtra, 411007, India
| | - Shubha S Manvi
- C2-83,84, MACS Agharkar Research Institute, G.G. Agarkar Road, Pune, Maharashtra, 411004, India
- Savitribai Phule Pune University, Ganeshkhind Road, Pune, Maharashtra, 411007, India
| | - Kajal Pardhi
- C2-83,84, MACS Agharkar Research Institute, G.G. Agarkar Road, Pune, Maharashtra, 411004, India
- Savitribai Phule Pune University, Ganeshkhind Road, Pune, Maharashtra, 411007, India
| | - Rahul A Bahulikar
- BAIF Development Research Foundation, Central Research Station, Urulikanchan, Pune, 412202, India
| | | | - Sanjana Patange
- Modern College, Shivajinagar, Pune, Maharashtra, 411005, India
| | - Mansi Joshi
- Fergusson College, F. C. Road, Pune, Maharashtra, 411004, India
| | | | - Monali C Rahalkar
- C2-83,84, MACS Agharkar Research Institute, G.G. Agarkar Road, Pune, Maharashtra, 411004, India.
- Savitribai Phule Pune University, Ganeshkhind Road, Pune, Maharashtra, 411007, India.
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3
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Wang M, Pu W, Wang S, Zeng X, Sui X, Wang X. pH-Related Changes in Soil Bacterial Communities in the Sanjiang Plain, Northeast China. Microorganisms 2023; 11:2950. [PMID: 38138094 PMCID: PMC10745975 DOI: 10.3390/microorganisms11122950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/16/2023] [Accepted: 11/28/2023] [Indexed: 12/24/2023] Open
Abstract
Soil bacteria are crucial components of terrestrial ecosystems, playing an important role in soil biogeochemical cycles. Although bacterial community diversity and composition are regulated by many abiotic and biotic factors, how soil physiochemical properties impact the soil bacteria community diversity and composition in wetland ecosystems remains largely unknown. In this study, we used high-throughput sequencing technology to investigate the diversity and composition of a soil bacterial community, as well as used the structural equation modeling (SEM) method to investigate the relationships of the soil's physicochemical properties (i.e., soil pH, soil organic carbon (SOC), total nitrogen (TN), ammonium nitrogen (NH4+N), electrical conductivity (EC) and nitrate nitrogen (NO3-N)), and soil bacterial community structures in three typical wetland sites in the Sanjiang Plain wetland. Our results showed that the soil physicochemical properties significantly changed the α and β-diversity of the soil bacteria communities, e.g., soil TN, NH4+N, NO3-N, and SOC were the main soil factors affecting the soil bacterial α-diversity. The soil TN and pH were the key soil factors affecting the soil bacterial community. Our results suggest that changes in soil pH indirectly affect soil bacterial communities by altering the soil nitrogenous nutrient content.
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Affiliation(s)
- Mingyu Wang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China; (M.W.); (W.P.); (S.W.)
| | - Wenmiao Pu
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China; (M.W.); (W.P.); (S.W.)
| | - Shenzheng Wang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China; (M.W.); (W.P.); (S.W.)
| | - Xiannan Zeng
- Institute of Crop Cultivation and Tillage, Heilongjiang Academy of Agricultural Sciences, Harbin 150088, China;
| | - Xin Sui
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China; (M.W.); (W.P.); (S.W.)
| | - Xin Wang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China; (M.W.); (W.P.); (S.W.)
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Petrosyan K, Thijs S, Piwowarczyk R, Ruraż K, Kaca W, Vangronsveld J. Diversity and potential plant growth promoting capacity of seed endophytic bacteria of the holoparasite Cistanche phelypaea (Orobanchaceae). Sci Rep 2023; 13:11835. [PMID: 37481658 PMCID: PMC10363106 DOI: 10.1038/s41598-023-38899-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 07/17/2023] [Indexed: 07/24/2023] Open
Abstract
Salt marshes are highly dynamic, biologically diverse ecosystems with a broad range of ecological functions. We investigated the endophytic bacterial community of surface sterilized seeds of the holoparasitic Cistanche phelypaea growing in coastal salt marshes of the Iberian Peninsula in Portugal. C. phelypaea is the only representative of the genus Cistanche that was reported in such habitat. Using high-throughput sequencing methods, 23 bacterial phyla and 263 different OTUs on genus level were found. Bacterial strains belonging to phyla Proteobacteria and Actinobacteriota were dominating. Also some newly classified or undiscovered bacterial phyla, unclassified and unexplored taxonomic groups, symbiotic Archaea groups inhabited the C. phelypaea seeds. γ-Proteobacteria was the most diverse phylogenetic group. Sixty-three bacterial strains belonging to Bacilli, Actinomycetes, α-, γ- and β-Proteobacteria and unclassified bacteria were isolated. We also investigated the in vitro PGP traits and salt tolerance of the isolates. Among the Actinobacteria, Micromonospora spp. showed the most promising endophytes in the seeds. Taken together, the results indicated that the seeds were inhabited by halotolerant bacterial strains that may play a role in mitigating the adverse effects of salt stress on the host plant. In future research, these bacteria should be assessed as potential sources of novel and unique bioactive compounds or as novel bacterial species.
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Affiliation(s)
- Kristine Petrosyan
- Department of Microbiology, Institute of Biology, Jan Kochanowski University, Uniwersytecka 7, 25-406, Kielce, Poland.
- Environmental Biology Research Group, Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590, Diepenbeek, Belgium.
| | - Sofie Thijs
- Environmental Biology Research Group, Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590, Diepenbeek, Belgium
| | - Renata Piwowarczyk
- Department of Environmental Biology, Center for Research and Conservation of Biodiversity, Institute of Biology, Jan Kochanowski University, Uniwersytecka 7, 25-406, Kielce, Poland
| | - Karolina Ruraż
- Department of Environmental Biology, Center for Research and Conservation of Biodiversity, Institute of Biology, Jan Kochanowski University, Uniwersytecka 7, 25-406, Kielce, Poland
| | - Wiesław Kaca
- Department of Microbiology, Institute of Biology, Jan Kochanowski University, Uniwersytecka 7, 25-406, Kielce, Poland
| | - Jaco Vangronsveld
- Environmental Biology Research Group, Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590, Diepenbeek, Belgium
- Department of Plant Physiology and Biophysics, Faculty of Biology and Biotechnology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Akademicka, 19, 20-033, Lublin, Poland
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5
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Jordan D, Kominoski JS, Servais S, Mills D. Salinity Impacts the Functional mcrA and dsrA Gene Abundances in Everglades Marshes. Microorganisms 2023; 11:1180. [PMID: 37317154 DOI: 10.3390/microorganisms11051180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 04/27/2023] [Accepted: 04/28/2023] [Indexed: 06/16/2023] Open
Abstract
Coastal wetlands, such as the Everglades, are increasingly being exposed to stressors that have the potential to modify their existing ecological processes because of global climate change. Their soil microbiomes include a population of organisms important for biogeochemical cycling, but continual stresses can disturb the community's composition, causing functional changes. The Everglades feature wetlands with varied salinity levels, implying that they contain microbial communities with a variety of salt tolerances and microbial functions. Therefore, tracking the effects of stresses on these populations in freshwater and brackish marshes is critical. The study addressed this by utilizing next generation sequencing (NGS) to construct a baseline soil microbial community. The carbon and sulfur cycles were studied by sequencing a microbial functional gene involved in each process, the mcrA and dsrA functional genes, respectively. Saline was introduced over two years to observe the taxonomic alterations that occurred after a long-term disturbance such as seawater intrusion. It was observed that saltwater dosing increased sulfite reduction in freshwater peat soils and decreased methylotrophy in brackish peat soils. These findings add to the understanding of microbiomes by demonstrating how changes in soil qualities impact communities both before and after a disturbance such as saltwater intrusion.
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Affiliation(s)
- Deidra Jordan
- Department of Biological Sciences, Florida International University, Miami, FL 33199, USA
- International Forensic Research Institute, Florida International University, Miami, FL 33199, USA
| | - John S Kominoski
- Department of Biological Sciences, Florida International University, Miami, FL 33199, USA
- Institute of the Environment, Florida International University, Miami, FL 33199, USA
| | - Shelby Servais
- Department of Biological Sciences, Florida International University, Miami, FL 33199, USA
- Institute of the Environment, Florida International University, Miami, FL 33199, USA
| | - DeEtta Mills
- Department of Biological Sciences, Florida International University, Miami, FL 33199, USA
- International Forensic Research Institute, Florida International University, Miami, FL 33199, USA
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6
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Keppeler FW, Junker JR, Shaw MJ, Alford SB, Engel AS, Hooper‐Bùi LM, Jensen OP, Lamb K, López‐Duarte PC, Martin CW, McDonald AM, Olin JA, Paterson AT, Polito MJ, Rabalais NN, Roberts BJ, Rossi RE, Swenson EM. Can biodiversity of preexisting and created salt marshes match across scales? An assessment from microbes to predators. Ecosphere 2023. [DOI: 10.1002/ecs2.4461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023] Open
Affiliation(s)
- Friedrich W. Keppeler
- Center for Limnology University of Wisconsin–Madison Madison Wisconsin USA
- Núcleo de Ecologia Aquática e Pesca da Amazônia Federal University of Pará Belém Pará Brazil
| | - James R. Junker
- Great Lakes Research Center Michigan Technological University Houghton Michigan USA
| | - Margaret J. Shaw
- Center for Limnology University of Wisconsin–Madison Madison Wisconsin USA
| | - Scott B. Alford
- Nature Coast Biological Station University of Florida Cedar Key Florida USA
| | - Annette S. Engel
- Department of Earth and Planetary Sciences The University of Tennessee–Knoxville Knoxville Tennessee USA
| | - Linda M. Hooper‐Bùi
- Department of Environmental Sciences Louisiana State University Baton Rouge Louisiana USA
| | - Olaf P. Jensen
- Center for Limnology University of Wisconsin–Madison Madison Wisconsin USA
| | - Katelyn Lamb
- Department of Oceanography and Coastal Sciences Louisiana State University Baton Rouge Louisiana USA
| | - Paola C. López‐Duarte
- Department of Biological Sciences University of North Carolina at Charlotte Charlotte North Carolina USA
| | - Charles W. Martin
- Nature Coast Biological Station University of Florida Cedar Key Florida USA
| | - Ashley M. McDonald
- Nature Coast Biological Station University of Florida Cedar Key Florida USA
| | - Jill A. Olin
- Great Lakes Research Center Michigan Technological University Houghton Michigan USA
| | - Audrey T. Paterson
- Department of Earth and Planetary Sciences The University of Tennessee–Knoxville Knoxville Tennessee USA
| | - Michael J. Polito
- Department of Oceanography and Coastal Sciences Louisiana State University Baton Rouge Louisiana USA
| | - Nancy N. Rabalais
- Department of Oceanography and Coastal Sciences Louisiana State University Baton Rouge Louisiana USA
| | | | - Ryann E. Rossi
- Louisiana Universities Marine Consortium Chauvin Louisiana USA
- St. Andrew and St. Joseph Bays Estuary Program Florida State University Panama City Panama City Florida USA
| | - Erick M. Swenson
- Department of Oceanography and Coastal Sciences Louisiana State University Baton Rouge Louisiana USA
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7
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Kim M, Park MS, Kang I, Cho JC. Thermomonas paludicola sp. nov., isolated from a lotus wetland. Int J Syst Evol Microbiol 2023; 73. [PMID: 36827191 DOI: 10.1099/ijsem.0.005737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
A Gram-stain-negative, aerobic, rod-shaped and motile bacterium, designated IMCC34681T, was isolated from a lotus wetland in the Republic of Korea. Cellular growth occurred at 10-37 °C (optimum, 30 °C), pH 6-9 (optimum, pH 7) and with 0-2 % (w/v) NaCl (optimum, 0.5 % NaCl). The results of 16S rRNA gene sequence analysis indicated that IMCC34681T represented a member of the genus Thermomonas, sharing 95.3-96.9 % similarities with type strains of species of the genus. The whole-genome sequence of IMCC34681T was 2.72 Mbp in size with 66.2 % DNA G+C content. The IMCC34681T genome shared the highest average nucleotide identity (ANI) value, 82.8 %, with that of Thermomonas brevis KACC 16975T among species of the genus Thermomonas, indicating that the strain represents a novel genomic species. The major respiratory quinone of the strain was ubiquinone-8 (Q-8) and the predominant cellular fatty acids were iso-C15 : 0 (25.7 %) and iso-C14 : 0 (20.8 %). The strain harboured diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified lipid as major fatty polar lipids. On the basis of the phylogenetic, phenotypic, chemotaxonomic and genomic characteristics, IMCC34681T was assigned to the genus Thermomonas as the type strain of a novel species, for which the name Thermomonas paludicola sp. nov. is proposed. The type strain is IMCC34681T (=KACC 21793T=NBRC 114635T).
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Affiliation(s)
- Mirae Kim
- Department of Biological Sciences and Bioengineering, Inha University, Incheon 22212, Republic of Korea
| | - Miri S Park
- Department of Biological Sciences and Bioengineering, Inha University, Incheon 22212, Republic of Korea
| | - Ilnam Kang
- Department of Biological Sciences and Bioengineering, Inha University, Incheon 22212, Republic of Korea
| | - Jang-Cheon Cho
- Department of Biological Sciences and Bioengineering, Inha University, Incheon 22212, Republic of Korea
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8
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Yu F, Zhang W, Hou X, Li Y, Tong J. How nutrient loads influence microbial-derived carbon accumulation in wetlands: A new insight from microbial metabolic investment strategies. ENVIRONMENTAL RESEARCH 2023; 217:114981. [PMID: 36460070 DOI: 10.1016/j.envres.2022.114981] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/13/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
Excessive anthropogenic nutrient inputs often lead to the degradation of wetland ecosystems and a decrease in carbon sink capacity. Microbial-derived carbon is increasingly recognized as an important precursor for organic carbon formation, which is controlled by the balance between microbial anabolic and catabolic processes. Shifts in microbial metabolic investment under nutrient load disturbance are key, but understudied, components of microbial-derived carbon turnover. Here, the roles of the distinct life-history traits and cooperation degree of key microbial assemblies in regulating microbial-derived carbon accumulation in a wetland receiving treated wastewater were firstly assessed by combining microbial biomarkers and genomic approaches. It was found that microbial-derived carbon was an important source of organic carbon in wetlands, and strongly associated with several microbial assemblies with specific trait strategies. Further analysis demonstrated that high growth yield strategists were mainly associated with microbial necromass accrual, while microbial biomass was more dominated by resource acquisition strategies in nutrient-imbalanced wetlands. A significant positive relationship between positive cohesion and microbial-derived carbon indicated that cooperative behavior among taxa promoted the production and accumulation of microbial-derived carbon. Moreover, resource stoichiometric balance, including C:N and C:P, was identified as an important driver of shifts in microbial metabolic investment strategies. The decreased C:N ratio led to a shift from resource acquisition strategies to high growth yield strategies for the microbial community, which facilitated microbial necromass accrual along the N-limited wetland, while the increased C:P ratio caused by excessive P deposition in sediments limits microbial cooperative growth to some extent. This study highlighted the importance of stoichiometric balance in mediating microbial growth metabolism and, in turn, enhancing the carbon sink capacity of wetlands.
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Affiliation(s)
- Feng Yu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Wenlong Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China.
| | - Xing Hou
- Institute of Water Science and Technology, Hohai University, Nanjing, 210098, PR China
| | - Yi Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China.
| | - Jiaxin Tong
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
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9
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Choi A, Cha IT, Lee KE, Son YK, Yu J, Seol D. The Role of Flavobacterium enshiense R6S-5-6 in the Wetland Ecosystem Revealed by Whole-Genome Analysis. Curr Microbiol 2023; 80:83. [PMID: 36680647 PMCID: PMC9867689 DOI: 10.1007/s00284-022-03157-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 11/25/2022] [Indexed: 01/22/2023]
Abstract
The wetland is an important ecosystem for purifying pollutants and circulating nutrients. Numerous microorganisms contribute to maintaining this function. We obtained Flavobacterium enshiense R6S-5-6 which was isolated from Ungok (Ramsar) Wetland and conducted whole-genome sequencing to investigate what contribution R6S-5-6 could make to the wetland community. The complete genome sequence of R6S-5-6 has a size of 3,251,289 bp with 37.68% of GC content. Gene annotation revealed that R6S-5-6 has several pathways to break down pollutants, including denitrification, assimilatory sulfate reduction (ASR), and polyphosphate-accumulating process. Furthermore, R6S-5-6 has genes that can have a positive effect on plants living in wetlands, such as storing essential nutrients, promoting plant growth, and protecting plants against pathogens.
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Affiliation(s)
- Ahhyeon Choi
- eGnome, Inc, 26 Beobwon-ro 9-Gil, Songpa-gu, Seoul, 05836 Republic of Korea
| | - In-Tae Cha
- grid.419519.10000 0004 0400 5474National Institute of Biological Resources, 42 Hwangyeong-ro, Seo-gu, Incheon, 22689 Republic of Korea
| | - Ki-Eun Lee
- grid.419519.10000 0004 0400 5474National Institute of Biological Resources, 42 Hwangyeong-ro, Seo-gu, Incheon, 22689 Republic of Korea
| | - Youn Kyoung Son
- grid.419519.10000 0004 0400 5474National Institute of Biological Resources, 42 Hwangyeong-ro, Seo-gu, Incheon, 22689 Republic of Korea
| | - Jaewoong Yu
- eGnome, Inc, 26 Beobwon-ro 9-Gil, Songpa-gu, Seoul, 05836 Republic of Korea
| | - Donghyeok Seol
- grid.31501.360000 0004 0470 5905Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 Republic of Korea ,grid.412480.b0000 0004 0647 3378Present Address: Department of Surgery, Seoul National University Bundang Hospital, 172 Dolma-ro, Bundang-gu, Seongnam, 13605 Republic of Korea
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10
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Abbott KM, Quirk T, Fultz LM. Soil microbial community development across a 32-year coastal wetland restoration time series and the relative importance of environmental factors. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 821:153359. [PMID: 35081409 DOI: 10.1016/j.scitotenv.2022.153359] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 01/19/2022] [Accepted: 01/19/2022] [Indexed: 06/14/2023]
Abstract
Soil microbes play key roles in ecosystem functioning through processes such as organic matter decomposition, nutrient and carbon cycling, and regulating vegetation structure and productivity. Coastal marshes are situated at the confluence of terrestrial and marine ecosystems; thus, their soils support abundant and diverse microbiota which facilitate globally important biogeochemical processes including nutrient cycling and greenhouse gas fluxes. With coastal marsh ecosystems threatened by relative sea level rise, subsidence, and development, mitigation for the loss of marshes is becoming commonplace. Despite the widespread implementation of marsh construction projects, little is known about the development and variability of microbial communities in created marshes. For this study, we tested the hypothesis that microbial community composition differs across created marshes of different ages and between created and natural marshes. We also hypothesized that the microbial community would be correlated with soil properties including soil organic carbon and nitrogen content, which were predicted to increase with marsh age. To test these hypotheses, we determined dominant microbial groups and environmental characteristics from six constructed marshes ranging in age from 0 to 32 years old, as well as an adjacent natural marsh. Our results revealed that microbial biomass estimates increased with marsh age except for the high elevation 20-year old marsh, yet each marsh contained a distinct microbial community composition. Across marshes, microbial community composition was significantly related to soil C:N ratio with an increase in total microbial abundance and actinomycetes and GM+ bacteria with an increase in soil C to N ratio. Additionally, shifts in dominant microbial groups were associated with differences in vegetation, elevation, and marsh age. The natural marsh community grouped more closely with younger rather than older marshes suggesting age is less important than environmental conditions. This study shows that microbial communities are not homogenized across restoration sites and do not necessarily converge to be similar to natural marshes over time. Local biotic and environmental conditions were correlated with microbial compositions, yet in seemingly similar conditions, microbial groups also differed. The effect of differences in microbial compositions on ecological functions are yet to be fully understood.
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Affiliation(s)
- Katherine M Abbott
- University of Massachusetts Amherst, Dept. of Environmental Conservation, 160 Holdsworth Way, Amherst, MA 01003, USA
| | - Tracy Quirk
- Louisiana State University, College of the Coast and Environment, Department of Oceanography and Coastal Sciences, Baton Rouge, LA, USA.
| | - Lisa M Fultz
- Louisiana State University AgCenter, School of Plant, Environmental and Soil Sciences, Baton Rouge, LA, USA
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11
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Almeida BK, Cline E, Sklar F, Afkhami ME. Hydrology shapes microbial communities and microbiome‐mediated growth of an Everglades tree island species. Restor Ecol 2022. [DOI: 10.1111/rec.13677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Brianna K. Almeida
- Department of Biology University of Miami Coral Gables Florida 33146 USA
| | - Eric Cline
- South Florida Water Management District West Palm Beach Florida 33406 USA
| | - Fred Sklar
- South Florida Water Management District West Palm Beach Florida 33406 USA
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12
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Zhu HZ, Jiang MZ, Zhou N, Jiang CY, Liu SJ. Submerged macrophytes recruit unique microbial communities and drive functional zonation in an aquatic system. Appl Microbiol Biotechnol 2021; 105:7517-7528. [PMID: 34519857 DOI: 10.1007/s00253-021-11565-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/21/2021] [Accepted: 09/01/2021] [Indexed: 11/30/2022]
Abstract
Aquatic and wetland systems are widely used for landscapes and water regeneration. Microbiomes and submerged macrophytes (hydrophytes) play essential roles in conversions of organic and inorganic compounds in those ecosystems. The systems were extensively investigated for microbial diversities and compositions. However, little is known about how hydrophytes recruited diverse microbiota and affected functional zonation in aquatic systems. To address this issue, epiphytic leaf and root, sediment, and surrounding water samples were collected from the dragon-shape aquatic system in Beijing Olympic Park. Metagenomic DNAs were extracted and subjected to sequencing. Results showed that epiphytic leaf and root microbiomes and metabolic marker genes were remarkably different from that of surrounding environment. Twenty indicator bacterial genera for epiphytic microbiomes were identified and 50 metabolic marker genes were applied to evaluate the function of epiphytic leaf and root, water, and sediment microbiomes. Co-occurrence analysis revealed highly modularized pattern of metabolic marker genes and indicator bacterial genera related to metabolic functions. These results suggested that hydrophytes shaped microbiomes and drove functional zonation in aquatic systems. KEY POINTS: • Microbiomes of hydrophytes and their surrounding environments were investigated. • Twenty indicator bacterial genera highly specific to epiphytic biofilms were identified. • Epiphytes recruited unique microbiomes and drove functional zonation in aquatic systems.
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Affiliation(s)
- Hai-Zhen Zhu
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beichen Xilu No.1, Chaoyang District, Beijing, 100101, People's Republic of China
| | - Min-Zhi Jiang
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beichen Xilu No.1, Chaoyang District, Beijing, 100101, People's Republic of China.,State Key Laboratory of Microbial Technology, Shandong University, Tsingdao, 266237, People's Republic of China
| | - Nan Zhou
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beichen Xilu No.1, Chaoyang District, Beijing, 100101, People's Republic of China
| | - Cheng-Ying Jiang
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beichen Xilu No.1, Chaoyang District, Beijing, 100101, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beichen Xilu No.1, Chaoyang District, Beijing, 100101, People's Republic of China. .,State Key Laboratory of Microbial Technology, Shandong University, Tsingdao, 266237, People's Republic of China. .,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.
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13
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Lamit LJ, Romanowicz KJ, Potvin LR, Lennon JT, Tringe SG, Chimner RA, Kolka RK, Kane ES, Lilleskov EA. Peatland microbial community responses to plant functional group and drought are depth-dependent. Mol Ecol 2021; 30:5119-5136. [PMID: 34402116 DOI: 10.1111/mec.16125] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 07/14/2021] [Accepted: 07/27/2021] [Indexed: 12/27/2022]
Abstract
Peatlands store one-third of Earth's soil carbon, the stability of which is uncertain due to climate change-driven shifts in hydrology and vegetation, and consequent impacts on microbial communities that mediate decomposition. Peatland carbon cycling varies over steep physicochemical gradients characterizing vertical peat profiles. However, it is unclear how drought-mediated changes in plant functional groups (PFGs) and water table (WT) levels affect microbial communities at different depths. We combined a multiyear mesocosm experiment with community sequencing across a 70-cm depth gradient, to test the hypotheses that vascular PFGs (Ericaceae vs. sedges) and WT (high vs. low) structure peatland microbial communities in depth-dependent ways. Several key results emerged. (i) Both fungal and prokaryote (bacteria and archaea) community structure shifted with WT and PFG manipulation, but fungi were much more sensitive to PFG whereas prokaryotes were much more sensitive to WT. (ii) PFG effects were largely driven by Ericaceae, although sedge effects were evident in specific cases (e.g., methanotrophs). (iii) Treatment effects varied with depth: the influence of PFG was strongest in shallow peat (0-10, 10-20 cm), whereas WT effects were strongest at the surface and middle depths (0-10, 30-40 cm), and all treatment effects waned in the deepest peat (60-70 cm). Our results underline the depth-dependent and taxon-specific ways that plant communities and hydrologic variability shape peatland microbial communities, pointing to the importance of understanding how these factors integrate across soil profiles when examining peatland responses to climate change.
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Affiliation(s)
- Louis J Lamit
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan, USA
| | - Karl J Romanowicz
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan, USA
| | - Lynette R Potvin
- USDA Forest Service Northern Research Station, Houghton, Michigan, USA
| | - Jay T Lennon
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Susannah G Tringe
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Rodney A Chimner
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan, USA
| | - Randall K Kolka
- USDA Forest Service Northern Research Station, Grand Rapids, Minnesota, USA
| | - Evan S Kane
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan, USA.,USDA Forest Service Northern Research Station, Houghton, Michigan, USA
| | - Erik A Lilleskov
- USDA Forest Service Northern Research Station, Houghton, Michigan, USA
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14
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Jeong SY, Kim TG. Effects of Plants on Metacommunities and Correlation Networks of Soil Microbial Groups in an Ecologically Restored Wetland. MICROBIAL ECOLOGY 2021; 81:657-672. [PMID: 33094372 DOI: 10.1007/s00248-020-01625-3] [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: 05/25/2020] [Accepted: 10/15/2020] [Indexed: 06/11/2023]
Abstract
Plants may influence different aspects of the belowground microorganisms, including abundance, distribution, and interaction, in wetlands. Microbial communities were scrutinized in a 4-year-old restored wetland ecosystem with 5 distinct sites: a bare-soil site (10 local patches) and sites dominated by Miscanthus, Phragmites, Typha, and Zizania (20 patches per site). Ordination analysis revealed that plant-induced attributes (e.g., organic matter and total carbon and nitrogen) could explain the total environmental variance. Community comparisons showed that all groups (Bacteria, Fungi, Protista, and Metazoa) differed in community structure among the 5 sites (P < 0.05). Comparisons between the community and environmental ordination plots revealed that community structural variation among the sites correlated with the environmental change across all groups (R2 ≥ 0.61). This indicates that all groups were primarily influenced by plant detritus. In addition, correlation networks markedly varied in topology and composition among the sites across all groups. There was a strong coupling between the metacommunity and correlation network for both Bacteria and Fungi (R2 ≥ 0.58), indicating that the plants determined the spatial covariation patterns of microbial populations. Multi-group networks and group synchrony results revealed that Bacteria, Fungi, and Protista were synchronized with each other (R2 ≥ 0.52) as the key founders of the microbial systems, while Metazoa participated in the system only under Miscanthus. Our findings concluded that the plants shaped the communities by controlling the abundance and interaction of their populations.
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Affiliation(s)
- So-Yeon Jeong
- Department of Microbiology, Pusan National University, Pusan, 46241, South Korea
| | - Tae Gwan Kim
- Department of Microbiology, Pusan National University, Pusan, 46241, South Korea.
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15
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Effects of Land Use and Pollution Loadings on Ecotoxicological Assays and Bacterial Taxonomical Diversity in Constructed Wetlands. DIVERSITY 2021. [DOI: 10.3390/d13040149] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Freshwater ecosystems are affected by anthropogenic alterations. Different studies have extensively studied the concentrations of metals, nutrients, and water quality as measurements of pollution in freshwater ecosystems. However, few studies have been able to link these pollutants to bioindicators as a risk assessment tool. This study aimed to examine the potential of two bioindicators, plant ecotoxicological assays and sediment bacterial taxonomic diversity, in ecological risk assessment for six freshwater constructed wetlands in a rapidly urbanizing watershed with diverse land uses. Sediment samples were collected summer, 2015 and 2017, and late summer and early fall in 2016 to conduct plant ecotoxicological assays based on plant (Lepidium, Sinapis and Sorghum) growth inhibition and identify bacterial taxonomical diversity by the 16S rRNA gene sequences. Concentrations of metals such as lead (Pb) and mercury (Hg) (using XRF), and nutrients such as nitrate and phosphate (using HACH DR 2800TM spectrophotometer) were measured in sediment and water samples respectively. Analyses of response patterns revealed that plant and bacterial bioindicators were highly responsive to variation in the concentrations of these pollutants. Hence, this opens up the scope of using these bioindicators for ecological risk assessment in constructed freshwater wetland ecosystems within urbanizing watersheds.
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16
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Li N, Chen X, Zhao H, Tang J, Jiang G, Li Z, Li X, Chen S, Zou S, Dong K, Xu Q. Spatial distribution and functional profile of the bacterial community in response to eutrophication in the subtropical Beibu Gulf, China. MARINE POLLUTION BULLETIN 2020; 161:111742. [PMID: 33075697 DOI: 10.1016/j.marpolbul.2020.111742] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 09/25/2020] [Accepted: 10/04/2020] [Indexed: 05/25/2023]
Abstract
In this study, we investigated the specific bacterial distribution and the response of bacterial communities to shifts in environmental factors in the subtropical Beibu Gulf, southern China. The abundances of Actinobacteria, Bacilli, Planctomycetia, Thermoleophilia, Anaerolineae, and Synechococcophycideae were significantly higher in high eutrophic samples than in medium eutrophic and oligotrophic samples. Bacterial alpha-diversity was found greater in high eutrophication samples than in the other samples. Besides, Ponticaulis koreensis, Nautella italic, Anaerospora hongkongensis, Candidatus Aquiluna rubra, and Roseovarius pacificus were sensitive to trophic variation and thus could be used as eco-markers. In addition, the relative abundances of functional genes involving carbohydrate and amino acid metabolism were very high among the samples. We also found temperature, Chl-a, TDN and NO3- were the main environmental drivers of bacterial community structure. Overall, this study provides new insight into the composition of bacterial community and function response to gradients of eutrophication in Beibu Gulf.
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Affiliation(s)
- Nan Li
- Key laboratory of Ministry of Education for Environment Change and Resources Use in Beibu Gulf, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, 175 East Mingxiu Road, Nanning 530001, Guangxi, People's Republic of China
| | - Xing Chen
- Key laboratory of Ministry of Education for Environment Change and Resources Use in Beibu Gulf, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, 175 East Mingxiu Road, Nanning 530001, Guangxi, People's Republic of China; College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning 530004, Guangxi, People's Republic of China
| | - Huaxian Zhao
- Key laboratory of Ministry of Education for Environment Change and Resources Use in Beibu Gulf, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, 175 East Mingxiu Road, Nanning 530001, Guangxi, People's Republic of China
| | - Jinli Tang
- Key laboratory of Ministry of Education for Environment Change and Resources Use in Beibu Gulf, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, 175 East Mingxiu Road, Nanning 530001, Guangxi, People's Republic of China
| | - Gonglingxia Jiang
- Key laboratory of Ministry of Education for Environment Change and Resources Use in Beibu Gulf, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, 175 East Mingxiu Road, Nanning 530001, Guangxi, People's Republic of China
| | - Zhuoting Li
- Key laboratory of Ministry of Education for Environment Change and Resources Use in Beibu Gulf, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, 175 East Mingxiu Road, Nanning 530001, Guangxi, People's Republic of China
| | - Xiaoli Li
- Key laboratory of Ministry of Education for Environment Change and Resources Use in Beibu Gulf, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, 175 East Mingxiu Road, Nanning 530001, Guangxi, People's Republic of China
| | - Si Chen
- College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning 530004, Guangxi, People's Republic of China
| | - Shuqi Zou
- Department of biological sciences, Kyonggi University, 154-42, Gwanggyosan-ro, Yeongtong-gu, Suwon-si, Gyeonggi-do 16227, South Korea
| | - Ke Dong
- Department of biological sciences, Kyonggi University, 154-42, Gwanggyosan-ro, Yeongtong-gu, Suwon-si, Gyeonggi-do 16227, South Korea
| | - Qiangsheng Xu
- Key laboratory of Ministry of Education for Environment Change and Resources Use in Beibu Gulf, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, 175 East Mingxiu Road, Nanning 530001, Guangxi, People's Republic of China.
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17
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Role of Microorganisms in the Remediation of Wastewater in Floating Treatment Wetlands: A Review. SUSTAINABILITY 2020. [DOI: 10.3390/su12145559] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
This article provides useful information for understanding the specific role of microbes in the pollutant removal process in floating treatment wetlands (FTWs). The current literature is collected and organized to provide an insight into the specific role of microbes toward plants and pollutants. Several aspects are discussed, such as important components of FTWs, common bacterial species, rhizospheric and endophytes bacteria, and their specific role in the pollutant removal process. The roots of plants release oxygen and exudates, which act as a substrate for microbial growth. The bacteria attach themselves to the roots and form biofilms to get nutrients from the plants. Along the plants, the microbial community also influences the performance of FTWs. The bacterial community contributes to the removal of nitrogen, phosphorus, toxic metals, hydrocarbon, and organic compounds. Plant–microbe interaction breaks down complex compounds into simple nutrients, mobilizes metal ions, and increases the uptake of pollutants by plants. The inoculation of the roots of plants with acclimatized microbes may improve the phytoremediation potential of FTWs. The bacteria also encourage plant growth and the bioavailability of toxic pollutants and can alleviate metal toxicity.
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18
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Zhao M, Ma YT, He SY, Mou X, Wu L. Dynamics of bacterioplankton community structure in response to seasonal hydrological disturbances in Poyang Lake, the largest wetland in China. FEMS Microbiol Ecol 2020; 96:5863183. [DOI: 10.1093/femsec/fiaa064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Accepted: 06/25/2020] [Indexed: 11/14/2022] Open
Abstract
ABSTRACT
Bacterioplankton communities play a critical role in biogeochemical cycling in freshwater environments, but how the hydrological regime impacts the assembly of bacterioplankton communities remains unclear. This study examined differences in bacterioplankton community structures between wet (July and September) and dry (October and November) seasons in two consecutive years (2016 and 2017) in Poyang Lake, the largest seasonal freshwater lake in China. Our results revealed no overall difference in bacterioplankton compositions and their predicted functions among spatially separated sites. However, bacterioplankton communities did show significant temporal shifts, mainly between samples in November and other months. Transitions from the dry to the wet season were observed in October in both sampling years. Meanwhile, insignificant spatial but significant temporal differences were also found for physicochemical variables. Moreover, redundancy analysis indicates that compared with water depth, water temperature was found to better explain changes in the bacterioplankton community. These findings consistently indicate that the bacterioplankton community in Poyang Lake is relatively less sensitive to annual hydrology shifts than water temperature and nutrient conditions.
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Affiliation(s)
- Man Zhao
- School of Life Science, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang 330022, China
| | - Yan-tian Ma
- School of Life Science, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang 330022, China
| | - Shi-yao He
- School of Life Science, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang 330022, China
| | - Xiaozhen Mou
- Department of Biological Sciences, Kent State University, OH 44242, USA
| | - Lan Wu
- School of Life Science, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang 330022, China
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19
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Wang Y, Cui H, Su X, Wei S, Zhu Y, Lu Z, Pang S, Liu H, Zhang S, Hou W. Diversity and Distribution of Methanogenic Community Between Two Typical Alpine Ecosystems on the Qinghai-Tibetan Plateau. Curr Microbiol 2020; 77:1061-1069. [PMID: 32036395 DOI: 10.1007/s00284-020-01891-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 01/18/2020] [Indexed: 11/29/2022]
Abstract
Alpine permafrost regions are important sources of biogenic CH4 and methanogens play an important role in the methane-producing process. The alpine permafrost on the Qinghai-Tibetan plateau comprises about one-sixth of China's land area, and there are various types of alpine ecosystems. However, the methanogenic communities in the typical alpine ecosystems are poorly understood. In this study, the active layers and permafrost layers of the natural ecosystem of alpine grassland (DZ2-1) and alpine swamp meadow (DZ2-5) were selected to investigate the diversity and abundance of methanogenic communities. Methanobacterium (63.65%) are overwhelmingly dominant in the active layer of the alpine grassland (DZ2-1A). ZC-I cluster (26.13%), RC-I cluster (19.56%), and Methanobacterium (15.02%) are the dominant groups in the permafrost layer of the alpine grassland (DZ2-1P). Methanosaeta (32.92%), Fen cluster (29.59%), Methanosarcina (16.33%), and Methanobacterium (13.95%) are the dominant groups in the active layer of the alpine swamp meadow (DZ2-5A), whereas the Fen cluster (50.85%), ZC-I cluster (27.63%), and RC-I cluster (14.15%) are relatively abundant in the permafrost layer of the alpine swamp meadow (DZ2-5P). qPCR data showed that the abundance of methanogens was higher in the natural ecosystem of alpine swamp meadow than in alpine grassland. We found that the community characteristics of methanogens were related to environmental factors. Pearson correlation analyses indicated that the relative abundance of Methanobacterium had a significantly positive correlation with hydrogen concentration (P < 0.01), while the relative abundances of Methanosaeta and Methanosarcina were positively correlated with acetate concentration (P < 0.05). This study will help us to understand the methanogenic communities and their surrounding environments in alpine ecosystems.
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Affiliation(s)
- Yanfa Wang
- School of Marine Sciences, China University of Geosciences, Beijing, 100083, China.,State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China
| | - Hongpeng Cui
- School of Marine Sciences, China University of Geosciences, Beijing, 100083, China.,State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China
| | - Xin Su
- School of Marine Sciences, China University of Geosciences, Beijing, 100083, China. .,State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China.
| | - Shiping Wei
- School of Marine Sciences, China University of Geosciences, Beijing, 100083, China
| | - Youhai Zhu
- Oil and Gas Survey, China Geological Survey, Beijing, 100083, China
| | - Zhenquan Lu
- Oil and Gas Survey, China Geological Survey, Beijing, 100083, China
| | - Shouji Pang
- Oil and Gas Survey, China Geological Survey, Beijing, 100083, China
| | - Hui Liu
- Oil and Gas Survey, China Geological Survey, Beijing, 100083, China
| | - Shuai Zhang
- Oil and Gas Survey, China Geological Survey, Beijing, 100083, China
| | - Weiguo Hou
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China
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20
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Abraham BS, Caglayan D, Carrillo NV, Chapman MC, Hagan CT, Hansen ST, Jeanty RO, Klimczak AA, Klingler MJ, Kutcher TP, Levy SH, Millard-Bruzos AA, Moore TB, Prentice DJ, Prescott ME, Roehm R, Rose JA, Yin M, Hyodo A, Lail K, Daum C, Clum A, Copeland A, Seshadri R, del Rio TG, Eloe-Fadrosh EA, Benskin JB. Shotgun metagenomic analysis of microbial communities from the Loxahatchee nature preserve in the Florida Everglades. ENVIRONMENTAL MICROBIOME 2020; 15:2. [PMID: 33902723 PMCID: PMC8067648 DOI: 10.1186/s40793-019-0352-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 12/21/2019] [Indexed: 06/12/2023]
Abstract
BACKGROUND Currently, much is unknown about the taxonomic diversity and the mechanisms of methane metabolism in the Florida Everglades ecosystem. The Loxahatchee National Wildlife Refuge is a section of the Florida Everglades that is almost entirely unstudied in regard to taxonomic profiling. This short report analyzes the metagenome of soil samples from this Refuge to investigate the predominant taxa, as well as the abundance of genes involved in environmentally significant metabolic pathways related to methane production (nitrogen fixation and dissimilatory sulfite reduction). METHODS Shotgun metagenomic sequencing using the Illumina platform was performed on 17 soil samples from four different sites within the Loxahatchee National Wildlife Refuge, and underwent quality control, assembly, and annotation. The soil from each sample was tested for water content and concentrations of organic carbon and nitrogen. RESULTS The three most common phyla of bacteria for every site were Actinobacteria, Acidobacteria, and Proteobacteria; however, there was variation in relative phylum composition. The most common phylum of Archaea was Euryarchaeota for all sites. Alpha and beta diversity analyses indicated significant congruity in taxonomic diversity in most samples from Sites 1, 3, and 4 and negligible congruity between Site 2 and the other sites. Shotgun metagenomic sequencing revealed the presence of biogeochemical biomarkers of particular interest (e.g., mrcA, nifH, and dsrB) within the samples. The normalized abundances of mcrA, nifH, and dsrB exhibited a positive correlation with nitrogen concentration and water content, and a negative correlation with organic carbon concentration. CONCLUSION This Everglades soil metagenomic study allowed examination of wetlands biological processes and showed expected correlations between measured organic constituents and prokaryotic gene frequency. Additionally, the taxonomic profile generated gives a basis for the diversity of prokaryotic microbial life throughout the Everglades.
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Affiliation(s)
| | - Deniz Caglayan
- Boca Raton Community High School, Boca Raton, FL 33486 USA
| | | | | | | | - Skye T. Hansen
- Boca Raton Community High School, Boca Raton, FL 33486 USA
| | | | | | | | | | - Sydney H. Levy
- Boca Raton Community High School, Boca Raton, FL 33486 USA
| | | | | | | | | | - Richard Roehm
- Boca Raton Community High School, Boca Raton, FL 33486 USA
| | - Jordan A. Rose
- Boca Raton Community High School, Boca Raton, FL 33486 USA
| | - Mulan Yin
- Boca Raton Community High School, Boca Raton, FL 33486 USA
| | - Ayumi Hyodo
- Department of Ecosystem Science and Management, Texas A&M University, College Station, TX 77843 USA
| | - Kathleen Lail
- Department of Energy, Joint Genome Institute, Berkeley, CA 94720 USA
| | - Christopher Daum
- Department of Energy, Joint Genome Institute, Berkeley, CA 94720 USA
| | - Alicia Clum
- Department of Energy, Joint Genome Institute, Berkeley, CA 94720 USA
| | - Alex Copeland
- Department of Energy, Joint Genome Institute, Berkeley, CA 94720 USA
| | - Rekha Seshadri
- Department of Energy, Joint Genome Institute, Berkeley, CA 94720 USA
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21
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Dedysh SN, Ivanova AA. Planctomycetes in boreal and subarctic wetlands: diversity patterns and potential ecological functions. FEMS Microbiol Ecol 2019; 95:5195516. [PMID: 30476049 DOI: 10.1093/femsec/fiy227] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 11/18/2018] [Indexed: 12/13/2022] Open
Abstract
Members of the phylum Planctomycetes are common inhabitants of boreal Sphagnum peat bogs and lichen-dominated tundra wetlands. These bacteria colonize both oxic and anoxic peat layers and reach the population size of 107 cells per gram of wet peat. The 16S rRNA gene sequences from planctomycetes comprise 5%-22% of total 16S rRNA gene reads retrieved from peat samples. Most abundant peat-inhabiting planctomycetes affiliate with the families Isosphaeraceae and Gemmataceae, and with as-yet-uncultured Phycisphaera-related group WD2101. The use of metatranscriptomics to assess the functional role of planctomycetes in peatlands suggested the presence of versatile hydrolytic capabilities in these bacteria. This evidence was further confirmed by the analysis of genome-encoded capabilities of isolates from wetlands. Large (up to 12 Mbp) genomes of planctomycetes encode wide repertoires of carbohydrate-active enzymes including many unclassified putative glycoside hydrolases, which suggests the presence of extremely high glycolytic potential in these bacteria. Experimental tests confirmed their ability to grow on xylan, pectin, starch, lichenan, cellulose, chitin and polysaccharides of microbial origin. These results provide an insight into the ecological roles of peat-inhabiting planctomycetes and suggest their participation in degradation of plant-derived polymers, exoskeletons of peat-inhabiting arthropods as well as exopolysaccharides produced by other bacteria.
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Affiliation(s)
- Svetlana N Dedysh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Leninsky prospect 33-2, Russia
| | - Anastasia A Ivanova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Leninsky prospect 33-2, Russia
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22
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Iliev I, Marhova M, Kostadinova S, Gochev V, Tsankova M, Ivanova A, Yahubyan G, Baev V. Metagenomic analysis of the microbial community structure in protected wetlands in the Maritza River Basin. BIOTECHNOL BIOTEC EQ 2019. [DOI: 10.1080/13102818.2019.1697364] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Affiliation(s)
- Ivan Iliev
- Faculty of Biology, Department of Biochemistry and Microbiology, University of Plovdiv, Plovdiv, Bulgaria
| | - Mariana Marhova
- Faculty of Biology, Department of Biochemistry and Microbiology, University of Plovdiv, Plovdiv, Bulgaria
| | - Sonya Kostadinova
- Faculty of Biology, Department of Biochemistry and Microbiology, University of Plovdiv, Plovdiv, Bulgaria
| | - Velizar Gochev
- Faculty of Biology, Department of Biochemistry and Microbiology, University of Plovdiv, Plovdiv, Bulgaria
| | - Marinela Tsankova
- Faculty of Biology, Department of Biochemistry and Microbiology, University of Plovdiv, Plovdiv, Bulgaria
| | - Angelina Ivanova
- Institute of Fisheries and Aquaculture, Agriculture Academy, Plovdiv, Bulgaria
| | - Galina Yahubyan
- Faculty of Biology, Department of Plant Physiology and Molecular Biology, University of Plovdiv, Plovdiv, Bulgaria
| | - Vesselin Baev
- Faculty of Biology, Department of Plant Physiology and Molecular Biology, University of Plovdiv, Plovdiv, Bulgaria
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Bonetti G, Trevathan-Tackett SM, Carnell PE, Macreadie PI. Implication of Viral Infections for Greenhouse Gas Dynamics in Freshwater Wetlands: Challenges and Perspectives. Front Microbiol 2019; 10:1962. [PMID: 31507569 PMCID: PMC6718870 DOI: 10.3389/fmicb.2019.01962] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 08/09/2019] [Indexed: 01/07/2023] Open
Abstract
Viruses are non-living, acellular entities, and the most abundant biological agents on earth. They are widely acknowledged as having the capacity to influence global biogeochemical cycles by infecting the bacterial and archaeal populations that regulate carbon and nutrient turnover. Evidence suggests that the majority of viruses in wetlands are bacteriophages, but despite their importance, studies on how viruses control the prokaryotic community and the concomitant impacts on ecosystem function (such as carbon cycling and greenhouse gas flux) in wetlands are rare. Here we investigate virus-prokaryote interactions in freshwater wetland ecosystems in the context of their potential influence on biogeochemical cycling. Specifically, we (1) synthesize existing literature to establish current understanding of virus-prokaryote interactions, focusing on the implications for wetland greenhouse gas dynamics and (2) identify future research priorities. Viral dynamics in freshwater wetlands have received much less attention compared to those in marine ecosystems. However, based on our literature review, within the last 10 years, viral ecology studies on freshwater wetlands have increased twofold. Despite this increase in literature, the potential implication of viral infections on greenhouse gas emission dynamics is still a knowledge gap. We hypothesize that the rate of greenhouse gas emissions and the pool of sequestered carbon could be strongly linked to the type and rate of viral infection. Viral replication mechanism choice will consequently influence the microbial efficiency of organic matter assimilation and thus the ultimate fate of carbon as a greenhouse gas or stored in soils.
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Affiliation(s)
- Giuditta Bonetti
- Faculty of Science, Engineering and Built Environment, School of Life and Environmental Sciences, Centre for Integrative Ecology, Deakin University, Burwood, VIC, Australia
| | - Stacey M Trevathan-Tackett
- Faculty of Science, Engineering and Built Environment, School of Life and Environmental Sciences, Centre for Integrative Ecology, Deakin University, Burwood, VIC, Australia
| | - Paul E Carnell
- Faculty of Science, Engineering and Built Environment, School of Life and Environmental Sciences, Centre for Integrative Ecology, Deakin University, Burwood, VIC, Australia
| | - Peter I Macreadie
- Faculty of Science, Engineering and Built Environment, School of Life and Environmental Sciences, Centre for Integrative Ecology, Deakin University, Burwood, VIC, Australia
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Aires T, Serebryakova A, Viard F, Serrão EA, Engelen AH. Acidification increases abundances of Vibrionales and Planctomycetia associated to a seaweed-grazer system: potential consequences for disease and prey digestion efficiency. PeerJ 2018; 6:e4377. [PMID: 29610702 PMCID: PMC5880178 DOI: 10.7717/peerj.4377] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 01/26/2018] [Indexed: 01/28/2023] Open
Abstract
Ocean acidification significantly affects marine organisms in several ways, with complex interactions. Seaweeds might benefit from rising CO2 through increased photosynthesis and carbon acquisition, with subsequent higher growth rates. However, changes in seaweed chemistry due to increased CO2 may change the nutritional quality of tissue for grazers. In addition, organisms live in close association with a diverse microbiota, which can also be influenced by environmental changes, with feedback effects. As gut microbiomes are often linked to diet, changes in seaweed characteristics and associated microbiome can affect the gut microbiome of the grazer, with possible fitness consequences. In this study, we experimentally investigated the effects of acidification on the microbiome of the invasive brown seaweed Sargassum muticum and a native isopod consumer Synisoma nadejda. Both were exposed to ambient CO2 conditions (380 ppm, pH 8.16) and an acidification treatment (1,000 ppm, pH 7.86) for three weeks. Microbiome diversity and composition were determined using high-throughput sequencing of the variable regions V5-7 of 16S rRNA. We anticipated that as a result of acidification, the seaweed-associated bacterial community would change, leading to further changes in the gut microbiome of grazers. However, no significant effects of elevated CO2 on the overall bacterial community structure and composition were revealed in the seaweed. In contrast, significant changes were observed in the bacterial community of the grazer gut. Although the bacterial community of S. muticum as whole did not change, Oceanospirillales and Vibrionales (mainly Pseudoalteromonas) significantly increased their abundance in acidified conditions. The former, which uses organic matter compounds as its main source, may have opportunistically taken advantage of the possible increase of the C/N ratio in the seaweed under acidified conditions. Pseudoalteromonas, commonly associated to diseased seaweeds, suggesting that acidification may facilitate opportunistic/pathogenic bacteria. In the gut of S. nadejda, the bacterial genus Planctomycetia increased abundance under elevated CO2. This shift might be associated to changes in food (S. muticum) quality under acidification. Planctomycetia are slow-acting decomposers of algal polymers that could be providing the isopod with an elevated algal digestion and availability of inorganic compounds to compensate the shifted C/N ratio under acidification in their food. In conclusion, our results indicate that even after only three weeks of acidified conditions, bacterial communities associated to ungrazed seaweed and to an isopod grazer show specific, differential shifts in associated bacterial community. These have potential consequences for seaweed health (as shown in corals) and isopod food digestion. The observed changes in the gut microbiome of the grazer seem to reflect changes in the seaweed chemistry rather than its microbial composition.
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Affiliation(s)
- Tania Aires
- Center for Marine Sciences (CCMAR), CIMAR, University of Algarve, Campus de Gambelas, Faro, Portugal
| | - Alexandra Serebryakova
- Center for Marine Sciences (CCMAR), CIMAR, University of Algarve, Campus de Gambelas, Faro, Portugal.,Sorbonne Université, CNRS, Lab Adaptation and Diversity in Marine Environments (UMR 7144 CNRS SU), Station Biologique de Roscoff, Roscoff, France
| | - Frédérique Viard
- Sorbonne Université, CNRS, Lab Adaptation and Diversity in Marine Environments (UMR 7144 CNRS SU), Station Biologique de Roscoff, Roscoff, France.,CNRS, UMR 7144, Divco Team, Station Biologique de Roscoff, Roscoff, France
| | - Ester A Serrão
- Center for Marine Sciences (CCMAR), CIMAR, University of Algarve, Campus de Gambelas, Faro, Portugal
| | - Aschwin H Engelen
- Center for Marine Sciences (CCMAR), CIMAR, University of Algarve, Campus de Gambelas, Faro, Portugal
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Cui H, Su X, Wei S, Zhu Y, Lu Z, Wang Y, Li Y, Liu H, Zhang S, Pang S. Comparative Analyses of Methanogenic and Methanotrophic Communities Between Two Different Water Regimes in Controlled Wetlands on the Qinghai-Tibetan Plateau, China. Curr Microbiol 2017; 75:484-491. [PMID: 29188321 DOI: 10.1007/s00284-017-1407-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 11/27/2017] [Indexed: 10/18/2022]
Abstract
Wetlands are an important methane (CH4) emission source. CH4 is mainly produced during the biogeochemical process, in which methanogens and methanotrophs both play important roles. However, little is known how these two microbial communities change under different water regimes. In this study, the diversity and abundance of methanogens and methanotrophs in wetlands on Qinghai-Tibetan Plateau with different water contents (a high water content site DZ2-14-3 and a low water content site DZ2-14-4) were studied by using phylogenetic analysis and quantitative PCR based on mcrA gene and pmoA gene. A total of 16 methanogenic operational taxonomic units (OTUs) and 9 methanotrophic OTUs are obtained. For methanogens, Fen cluster (58.0%) and Methanosaetaceae (20.3%) are the dominant groups in high moisture samples, whereas Methanosaetaceae (32.4%), Methanosarcinaceae (29.4%), and Methanobacteriaceae (22.1%) are prevalent in low moisture samples. Methylobacter (90.0%) of type I methanotrophs are overwhelmingly dominant in high moisture samples, while Methylocystis (53.3%) and Methylomonas (42.2%) belonging to types II and I methanotrophs are the predominant groups in low moisture samples. Furthermore, qPCR analysis revealed that the abundance of methanogens and methanotrophs were higher in high moisture samples than that in low moisture samples. Overall, this comparative study between wetlands controlled by two different water regimes on the Qinghai-Tibetan Plateau provides fundamental data for further research on microbial functions within extreme ecosystems.
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Affiliation(s)
- Hongpeng Cui
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China.,School of Marine Sciences, China University of Geosciences, Beijing, 100083, China
| | - Xin Su
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China. .,School of Marine Sciences, China University of Geosciences, Beijing, 100083, China.
| | - Shiping Wei
- School of Marine Sciences, China University of Geosciences, Beijing, 100083, China
| | - Youhai Zhu
- Oil and Gas Survey, China Geological Survey, Beijing, 100029, China
| | - Zhenquan Lu
- Oil and Gas Survey, China Geological Survey, Beijing, 100029, China
| | - Yanfa Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China.,School of Marine Sciences, China University of Geosciences, Beijing, 100083, China
| | - Yuejiao Li
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China.,School of Marine Sciences, China University of Geosciences, Beijing, 100083, China
| | - Hui Liu
- Oil and Gas Survey, China Geological Survey, Beijing, 100029, China
| | - Shuai Zhang
- Oil and Gas Survey, China Geological Survey, Beijing, 100029, China
| | - Shouji Pang
- Oil and Gas Survey, China Geological Survey, Beijing, 100029, China
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Methanogenesis in oxygenated soils is a substantial fraction of wetland methane emissions. Nat Commun 2017; 8:1567. [PMID: 29146959 PMCID: PMC5691036 DOI: 10.1038/s41467-017-01753-4] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 10/11/2017] [Indexed: 01/04/2023] Open
Abstract
The current paradigm, widely incorporated in soil biogeochemical models, is that microbial methanogenesis can only occur in anoxic habitats. In contrast, here we show clear geochemical and biological evidence for methane production in well-oxygenated soils of a freshwater wetland. A comparison of oxic to anoxic soils reveal up to ten times greater methane production and nine times more methanogenesis activity in oxygenated soils. Metagenomic and metatranscriptomic sequencing recover the first near-complete genomes for a novel methanogen species, and show acetoclastic production from this organism was the dominant methanogenesis pathway in oxygenated soils. This organism, Candidatus Methanothrix paradoxum, is prevalent across methane emitting ecosystems, suggesting a global significance. Moreover, in this wetland, we estimate that up to 80% of methane fluxes could be attributed to methanogenesis in oxygenated soils. Together, our findings challenge a widely held assumption about methanogenesis, with significant ramifications for global methane estimates and Earth system modeling.
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Lynn TM, Ge T, Yuan H, Wei X, Wu X, Xiao K, Kumaresan D, Yu SS, Wu J, Whiteley AS. Soil Carbon-Fixation Rates and Associated Bacterial Diversity and Abundance in Three Natural Ecosystems. MICROBIAL ECOLOGY 2017; 73:645-657. [PMID: 27838764 DOI: 10.1007/s00248-016-0890-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 10/27/2016] [Indexed: 05/03/2023]
Abstract
CO2 assimilation by autotrophic microbes is an important process in soil carbon cycling, and our understanding of the community composition of autotrophs in natural soils and their role in carbon sequestration of these soils is still limited. Here, we investigated the autotrophic C incorporation in soils from three natural ecosystems, i.e., wetland (WL), grassland (GR), and forest (FO) based on the incorporation of labeled C into the microbial biomass. Microbial assimilation of 14C (14C-MBC) differed among the soils from three ecosystems, accounting for 14.2-20.2% of 14C-labeled soil organic carbon (14C-SOC). We observed a positive correlation between the cbbL (ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) large-subunit gene) abundance, 14C-SOC level, and 14C-MBC concentration confirming the role of autotrophic bacteria in soil carbon sequestration. Distinct cbbL-bearing bacterial communities were present in each soil type; form IA and form IC RubisCO-bearing bacteria were most abundant in WL, followed by GR soils, with sequences from FO soils exclusively derived from the form IC clade. Phylogenetically, the diversity of CO2-fixing autotrophs and CO oxidizers differed significantly with soil type, whereas cbbL-bearing bacterial communities were similar when assessed using coxL. We demonstrate that local edaphic factors such as pH and salinity affect the C-fixation rate as well as cbbL and coxL gene abundance and diversity. Such insights into the effect of soil type on the autotrophic bacterial capacity and subsequent carbon cycling of natural ecosystems will provide information to enhance the sustainable management of these important natural ecosystems.
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Affiliation(s)
- Tin Mar Lynn
- Key Laboratory of Agro-ecological Processes in Subtropical Region & Changsha Observation and Research Station for Agricultural Environment, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan Province, 410125, China
- Biotechnology Research Department, Ministry of Education, Kyaukse, Myanmar
| | - Tida Ge
- Key Laboratory of Agro-ecological Processes in Subtropical Region & Changsha Observation and Research Station for Agricultural Environment, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan Province, 410125, China.
- UWA-CAS Joint Laboratory in Soil System Science, Changsha, 410125, China.
| | - Hongzhao Yuan
- Key Laboratory of Agro-ecological Processes in Subtropical Region & Changsha Observation and Research Station for Agricultural Environment, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan Province, 410125, China
| | - Xiaomeng Wei
- Key Laboratory of Agro-ecological Processes in Subtropical Region & Changsha Observation and Research Station for Agricultural Environment, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan Province, 410125, China
| | - Xiaohong Wu
- Key Laboratory of Agro-ecological Processes in Subtropical Region & Changsha Observation and Research Station for Agricultural Environment, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan Province, 410125, China
| | - Keqing Xiao
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, NyMunkegade 114, 8000, Aarhus C, Denmark
| | - Deepak Kumaresan
- UWA-CAS Joint Laboratory in Soil System Science, Changsha, 410125, China
- School of Earth and Environment, The University of Western Australia, Crawley, WA, 6009, Australia
| | - San San Yu
- Biotechnology Research Department, Ministry of Education, Kyaukse, Myanmar
| | - Jinshui Wu
- Key Laboratory of Agro-ecological Processes in Subtropical Region & Changsha Observation and Research Station for Agricultural Environment, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan Province, 410125, China
- UWA-CAS Joint Laboratory in Soil System Science, Changsha, 410125, China
| | - Andrew S Whiteley
- Key Laboratory of Agro-ecological Processes in Subtropical Region & Changsha Observation and Research Station for Agricultural Environment, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan Province, 410125, China
- UWA-CAS Joint Laboratory in Soil System Science, Changsha, 410125, China
- School of Earth and Environment, The University of Western Australia, Crawley, WA, 6009, Australia
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28
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Chen X, Yang J, Zhu X, Liang X, Lei Y, He C. N-fixing trees in wetland restoration plantings: effects on nitrogensupply and soil microbial communities. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:24749-24757. [PMID: 27658403 DOI: 10.1007/s11356-016-7454-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 08/10/2016] [Indexed: 06/06/2023]
Abstract
To investigate the impact of an exotic Frankia nodulated tree (Alnus trabeculosa) on soil nitrogen content, soil microbial composition, and the abundance of N turnover-related functional microorganism community, we compared the community structure and abundance of key functional genes (nifH, bacterial/archaeal amoA, and nosZ) in the rhizosphere and nonrhizosphere of monoculture of Phragmites australis and A.trabeculosa-P.australis mixed communities by MiSeq Illumina sequencing and real-time PCR, respectively. The introduction of Frankia nodulated tree to recover degraded wetland was effective in the accumulation of soil organic carbon and nitrogen, which was the key factor to impact on the bacterial community composition revealed by canonical correspondence analysis. Acidobacteria and Proteobacteria were the dominant bacterial phylums while seven rare phyla appeared the most phylogenetically different among the investigated soil of two vegetations, including Chlorobi, Cyanobacteria, OD1, OP11, TM6, TM7, and GN02. The gene copy numbers of nifH were ranged from 2.28 × 108 to 2.96 × 109 copies g-1 dry soil in the wetland, and which were significantly higher in soil samples from P. australis than that from A.trabeculosa. While the abundance of nosZ in both rhizosphere and nonrhizosphere soils of A.trabeculosa-P.australis mixed communities was significantly lower compared with P.australis monoculture. The potential nitrification (PNA) (0.15-0.41 mg NOx-N kg-1 dry soil d-1) in the rhizosphere of A. trabeculosa was significantly higher than that of P. australis, and the soil denitrification enzyme activity (DEA) (0.42-0.90 nmol N2O-N g-1 dry soil h-1) was lower in the mixed community compared with monoculture of P. australis. The introduced planting of Frankia nodulated tree effectively accumulated soil organic carbon and nitrogen and reduce the relative abundance and activity of nitrogen-fixing bacteria and denitrification bacteria.
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Affiliation(s)
- XuePing Chen
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 20072, People's Republic of China
| | - JunNa Yang
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 20072, People's Republic of China
| | - XiE Zhu
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 20072, People's Republic of China
| | - Xia Liang
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 20072, People's Republic of China
| | - YanRu Lei
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 20072, People's Republic of China
| | - ChiQuan He
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 20072, People's Republic of China.
- , 150#, 99 Shangda Road, Shanghai, 200444, China.
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29
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Secker NH, Chua JPS, Laurie RE, McNoe L, Guy PL, Orlovich DA, Summerfield TC. Characterization of the cyanobacteria and associated bacterial community from an ephemeral wetland in New Zealand. JOURNAL OF PHYCOLOGY 2016; 52:761-773. [PMID: 27262053 DOI: 10.1111/jpy.12434] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Accepted: 04/21/2016] [Indexed: 06/05/2023]
Abstract
New Zealand ephemeral wetlands are ecologically important, containing up to 12% of threatened native plant species and frequently exhibiting conspicuous cyanobacterial growth. In such environments, cyanobacteria and associated heterotrophs can influence primary production and nutrient cycling. Wetland communities, including bacteria, can be altered by increased nitrate and phosphate due to agricultural practices. We have characterized cyanobacteria from the Wairepo Kettleholes Conservation Area and their associated bacteria. Use of 16S rRNA amplicon sequencing identified several operational taxonomic units (OTUs) representing filamentous heterocystous and non-heterocystous cyanobacterial taxa. One Nostoc OTU that formed macroscopic colonies dominated the cyanobacterial community. A diverse bacterial community was associated with the Nostoc colonies, including a core microbiome of 39 OTUs. Identity of the core microbiome associated with macroscopic Nostoc colonies was not changed by the addition of nutrients. One OTU was highly represented in all Nostoc colonies (27.6%-42.6% of reads) and phylogenetic analyses identified this OTU as belonging to the genus Sphingomonas. Scanning electron microscopy showed the absence of heterotrophic bacteria within the Nostoc colony but revealed a diverse community associated with the colonies on the external surface.
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Affiliation(s)
- Nick H Secker
- Department of Botany, University of Otago, Dunedin, New Zealand
| | | | - Rebecca E Laurie
- Otago Genomics and Bioinformatics Facility, University of Otago, Dunedin, New Zealand
| | - Les McNoe
- Otago Genomics and Bioinformatics Facility, University of Otago, Dunedin, New Zealand
| | - Paul L Guy
- Department of Botany, University of Otago, Dunedin, New Zealand
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Correlating microbial community with physicochemical indices and structures of a full-scale integrated constructed wetland system. Appl Microbiol Biotechnol 2016; 100:6917-6926. [DOI: 10.1007/s00253-016-7526-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 03/30/2016] [Accepted: 04/05/2016] [Indexed: 10/21/2022]
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31
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Effect of Plant Harvesting on the Performance of Constructed Wetlands during Summer. WATER 2016. [DOI: 10.3390/w8010024] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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32
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Site history and edaphic features override the influence of plant species on microbial communities in restored tidal freshwater wetlands. Appl Environ Microbiol 2015; 81:3482-91. [PMID: 25769832 DOI: 10.1128/aem.00038-15] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 03/07/2015] [Indexed: 11/20/2022] Open
Abstract
Restored wetland soils differ significantly in physical and chemical properties from their natural counterparts even when plant community compositions are similar, but effects of restoration on microbial community composition and function are not well understood. Here, we investigate plant-microbe relationships in restored and natural tidal freshwater wetlands from two subestuaries of the Chesapeake Bay. Soil samples were collected from the root zone of Typha latifolia, Phragmites australis, Peltandra virginica, and Lythrum salicaria. Soil microbial composition was assessed using 454 pyrosequencing, and genes representing bacteria, archaea, denitrification, methanogenesis, and methane oxidation were quantified. Our analysis revealed variation in some functional gene copy numbers between plant species within sites, but intersite comparisons did not reveal consistent plant-microbe trends. We observed more microbial variations between plant species in natural wetlands, where plants have been established for a long period of time. In the largest natural wetland site, sequences putatively matching methanogens accounted for ∼17% of all sequences, and the same wetland had the highest numbers of genes coding for methane coenzyme A reductase (mcrA). Sequences putatively matching aerobic methanotrophic bacteria and anaerobic methane-oxidizing archaea (ANME) were detected in all sites, suggesting that both aerobic and anaerobic methane oxidation are possible in these systems. Our data suggest that site history and edaphic features override the influence of plant species on microbial communities in restored wetlands.
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Microbial diversity in hummock and hollow soils of three wetlands on the Qinghai-Tibetan Plateau revealed by 16S rRNA pyrosequencing. PLoS One 2014; 9:e103115. [PMID: 25078273 PMCID: PMC4117511 DOI: 10.1371/journal.pone.0103115] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 06/27/2014] [Indexed: 11/19/2022] Open
Abstract
The wetlands of the Qinghai-Tibetan Plateau are believed to play an important role in global nutrient cycling, but the composition and diversity of microorganisms in this ecosystem are poorly characterized. An understanding of the effects of geography and microtopography on microbial populations will provide clues to the underlying mechanisms that structure microbial communities. In this study, we used pyrosequencing-based analysis of 16S rRNA gene sequences to assess and compare the composition of soil microbial communities present in hummock and hollow soils from three wetlands (Dangxiong, Hongyuan and Maduo) on the Qinghai-Tibetan Plateau, the world's highest plateau. A total of 36 bacterial phyla were detected. Proteobacteria (34.5% average relative abundance), Actinobacteria (17.3%) and Bacteroidetes (11%) had the highest relative abundances across all sites. Chloroflexi, Acidobacteria, Verrucomicrobia, Firmicutes, and Planctomycetes were also relatively abundant (1-10%). In addition, archaeal sequences belonging to Euryarchaea, Crenarchaea and Thaumarchaea were detected. Alphaproteobacteria sequences, especially of the order Rhodospirillales, were significantly more abundant in Maduo than Hongyuan and Dangxiong wetlands. Compared with Hongyuan soils, Dangxiong and Maduo had significantly higher relative abundances of Gammaproteobacteria sequences (mainly order Xanthomonadales). Hongyuan wetland had a relatively high abundance of methanogens (mainly genera Methanobacterium, Methanosarcina and Methanosaeta) and methanotrophs (mainly Methylocystis) compared with the other two wetlands. Principal coordinate analysis (PCoA) indicated that the microbial community structure differed between locations and microtopographies and canonical correspondence analysis indicated an association between microbial community structure and soil properties or geography. These insights into the microbial community structure and the main controlling factors in wetlands of the Qinghai-Tibetan Plateau provide a valuable background for further studies on biogeochemical processes in this distinct ecosystem.
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