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Gómez-Acata ES, Teutli C, Falcón LI, García-Maldonado JQ, Prieto-Davó A, Yanez-Montalvo A, Cadena S, Chiappa-Carrara X, Herrera-Silveira JA. Sediment microbial community structure associated to different ecological types of mangroves in Celestún, a coastal lagoon in the Yucatan Peninsula, Mexico. PeerJ 2023; 11:e14587. [PMID: 36785710 PMCID: PMC9921989 DOI: 10.7717/peerj.14587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 11/28/2022] [Indexed: 02/11/2023] Open
Abstract
Mangroves are unique coastal ecosystems, which have many important ecological functions, as they are a reservoir of many marine species well adapted to saline conditions and are fundamental as sites of carbon storage. Although the microbial contribution to nutrient cycling in these ecosystems has been well recognized, there is a lack of information regarding the microbial composition and structure of different ecological types of mangrove forests. In this study, we characterized the microbial community (Bacteria and Archaea) in sediments associated with five ecological types of mangrove forests in a coastal lagoon dominated by Avicennia germinans and Rhizophora mangle, through 16S rRNA-V4 gene sequencing. Overall, Proteobacteria (51%), Chloroflexi (12%), Gemmatimonadetes (5%) and Planctomycetes (6%) were the most abundant bacterial phyla, while Thaumarchaeota (30%), Bathyarchaeota (21%) and Nanoarchaeaeota (18%) were the dominant archaeal phyla. The microbial composition associated with basin mangroves dominated by Avicennia germinans was significantly different from the other ecological types, which becomes relevant for restoration strategies.
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Affiliation(s)
| | - Claudia Teutli
- Escuela Nacional de Estudios Superiores, Mérida, Yucatán, México,Laboratorio Nacional de Resiliencia Costera (LANRESC), Sisal, Yucatán, México
| | | | - José Q. García-Maldonado
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán, México
| | | | | | - Santiago Cadena
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán, México
| | - Xavier Chiappa-Carrara
- Escuela Nacional de Estudios Superiores, Mérida, Yucatán, México,Unidad Multidisciplinaria de Docencia e Investigación, Unidad Sisal, Universidad Nacional Autónoma de México, Sisal, Yucatán, México
| | - Jorge A. Herrera-Silveira
- Laboratorio Nacional de Resiliencia Costera (LANRESC), Sisal, Yucatán, México,Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán, México
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2
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Zhang X, Chen Z, Yu Y, Liu Z, Mo L, Sun Z, Lin Z, Wang J. Response of bacterial diversity and community structure to metals in mangrove sediments from South China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 850:157969. [PMID: 35985575 DOI: 10.1016/j.scitotenv.2022.157969] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/25/2022] [Accepted: 08/07/2022] [Indexed: 06/15/2023]
Abstract
Human activities have given rise to metal contamination in the constituents of mangrove ecosystems, posing a critical threat to sediment microorganisms; hence, it is of great importance to comprehend the effects of metals on the microbial communities in mangrove sediments. This study was the first to explore the response of the bacterial diversity and community structure to nine metals (As, Co, Cr, Cu, Mn, Ni, Pb, V and Zn) and organic matter fractions (including total organic carbon (TOC), total nitrogen (TN), and total sulfur (TS)) in mangrove wetlands from Zhanjiang, China, using 16S rRNA high-throughput sequencing technology and Spearman correlation analysis. The results showed that these nine metals were scattered differently in different mangrove sediments, and the metals and organic matter fractions jointly affected the bacterial communities in the sediments. Several metals displayed significant positive correlations with the abundances of the phylum Bacteroidetes and the genera Actibacter and Sphingobacterium but significant negative correlations with the abundances of two genera Holophaga and Caldithrix. Furthermore, the abundances of the phylum Actinobacteria and many bacterial genera showed significant positive or negative responses to the levels of the three organic matter fractions. Interestingly, the levels of a number of bacterial genera that exhibited increased abundance with high levels of metals and TS might be reduced with high TOC and TN, and vice versa: the levels of genera that exhibited decreased abundance with high levels of metals and TS might be increased with high TOC and TN. Overall, many bacterial groups showed different response patterns to each metal or organic matter fraction, and these metals together with organic matter fractions influenced the bacterial diversity and community structure in mangrove sediments.
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Affiliation(s)
- Xiaoyong Zhang
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Zihui Chen
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Youkai Yu
- Institute for Innovation and Entrepreneurship, Loughborough University, London E20 3BS, UK
| | - Zhiying Liu
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Li Mo
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Zuwang Sun
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Zhongmei Lin
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Jun Wang
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China.
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3
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Kumar M, Kumar R, Chaudhary DR, Jha B. An appraisal of early stage biofilm-forming bacterial community assemblage and diversity in the Arabian Sea, India. MARINE POLLUTION BULLETIN 2022; 180:113732. [PMID: 35594757 DOI: 10.1016/j.marpolbul.2022.113732] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 05/01/2022] [Accepted: 05/02/2022] [Indexed: 06/15/2023]
Abstract
The community composition and distribution of early-stage (24 h) biofilm-forming bacteria on two different surfaces (glass slide and polystyrene plastic slide) at three different locations (Diu, Alang and Sikka) were studied using a culture-dependent and next-generation sequencing (NGS) approach in the Arabian Sea, Gujarat, India. The most dominant phyla observed using the NGS approach were the Proteobacteria among the sampling sites. Gammaproteobacteria class dominated both the surfaces among the sites and accounted for 46.7% to 89.2% of total abundance. The culture-dependent analysis showed Proteobacteria and Firmicutes as the dominant phyla on the surfaces within the sampling sites. During the initial colonization, hydrocarbon-degrading bacterial strains have also attached to the surfaces. The outcome of this study would be of great importance for targeting the early stage biofilm-forming and hydrocarbon-degrading bacterial isolates may help to degrade plastic in the marine environment.
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Affiliation(s)
- Madhav Kumar
- CSIR - Central Salt and Marine Chemicals Research Institute, G. B. Bhavnagar, Gujarat 364 002, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India
| | - Raghawendra Kumar
- CSIR - Central Salt and Marine Chemicals Research Institute, G. B. Bhavnagar, Gujarat 364 002, India
| | - Doongar R Chaudhary
- CSIR - Central Salt and Marine Chemicals Research Institute, G. B. Bhavnagar, Gujarat 364 002, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India.
| | - Bhavanath Jha
- CSIR - Central Salt and Marine Chemicals Research Institute, G. B. Bhavnagar, Gujarat 364 002, India.
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4
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Xia D, Zhao H, Kobayashi S, Mi Q, Hao A, Iseri Y. Effect of remediation reagents on bacterial composition and ecological function in black-odorous water sediments. Arch Microbiol 2022; 204:280. [PMID: 35462604 PMCID: PMC9035426 DOI: 10.1007/s00203-022-02871-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 03/22/2022] [Accepted: 03/23/2022] [Indexed: 11/20/2022]
Abstract
Black-odorous urban water bodies and sediments pose a serious environmental problem. In this study, we conducted microcosm batch experiments to investigate the effect of remediation reagents (magnesium hydroxide and calcium nitrate) on native bacterial communities and their ecological functions in the black-odorous sediment of urban water. The dominant phyla (Proteobacteria, Actinobacteria, Chloroflexi, and Planctomycetes) and classes (Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria, Actinobacteria, Anaerolineae, and Planctomycetia) were determined under calcium nitrate and magnesium hydroxide treatments. Functional groups related to aerobic metabolism, including aerobic chemoheterotrophy, dark sulfide oxidation, and correlated dominant genera (Thiobacillus, Lysobacter, Gp16, and Gaiella) became more abundant under calcium nitrate treatment, whereas functional genes potentially involved in dissimilatory sulfate reduction became less abundant. The relative abundance of chloroplasts, fermentation, and correlated genera (Desulfomonile and unclassified Cyanobacteria) decreased under magnesium hydroxide treatment. Overall, these results indicated that calcium nitrate addition improved hypoxia-related reducing conditions in the sediment and promoted aerobic chemoheterotrophy.
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Kruppa OC, Gerlach D, Fan R, Czermak P. Development of a chemically defined medium for Planctopirus limnophila to increase biomass production. ELECTRON J BIOTECHN 2021. [DOI: 10.1016/j.ejbt.2021.09.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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6
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Semanti P, Robin RS, Purvaja R, Ramesh R. Fatty acid signatures of sediment microbial community in the chronically polluted mangrove ecosystem. MARINE POLLUTION BULLETIN 2021; 172:112885. [PMID: 34461371 DOI: 10.1016/j.marpolbul.2021.112885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 08/14/2021] [Accepted: 08/17/2021] [Indexed: 06/13/2023]
Abstract
Phospholipid fatty acid (PLFA) analysis was used to examine variation in the distribution of microbial communities in heavily polluted mangrove sediments of Thane creek, west coast of India. A total of 40 individual PLFAs representing 11 functional groups were identified in the sediment and were mainly dominated by saturated fatty acids (anaerobic prokaryotes) >50%. Significant dominance of PUFA, 16:3 ω6c (34.2%) indicators of micro-eukaryotes, in subsurface depth (p < 0.05) suggests input from the remnants of marine microalgae. Declined mean relative abundance of fungi (<6%) and actinomycetes (<1%) were detected in the sediment indicating their sensitivity to anthropic stressors. Homogenous profile of microbial diversity indicating active bioturbation. Cumulative metabolic stress evident from SAT/MUFA (>1), B/F (>1) and G+/G- (<1) ratio and prolonged hypoxia to be prevalent in the creek during the study. In conclusion, PLFA signatures can thus be used as potential biomarkers of environmental monitoring and proxy for interpreting ecosystem health.
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Affiliation(s)
- P Semanti
- National Centre for Sustainable Coastal Management, Ministry of Environment, Forest and Climate Change, Chennai 600 025, India
| | - R S Robin
- National Centre for Sustainable Coastal Management, Ministry of Environment, Forest and Climate Change, Chennai 600 025, India
| | - R Purvaja
- National Centre for Sustainable Coastal Management, Ministry of Environment, Forest and Climate Change, Chennai 600 025, India
| | - R Ramesh
- National Centre for Sustainable Coastal Management, Ministry of Environment, Forest and Climate Change, Chennai 600 025, India.
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7
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De Santana CO, Spealman P, Melo V, Gresham D, de Jesus T, Oliveira E, Chinalia FA. Large-scale differences in diversity and functional adaptations of prokaryotic communities from conserved and anthropogenically impacted mangrove sediments in a tropical estuary. PeerJ 2021; 9:e12229. [PMID: 34631324 PMCID: PMC8465992 DOI: 10.7717/peerj.12229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 09/08/2021] [Indexed: 12/24/2022] Open
Abstract
Mangroves are tropical ecosystems with strategic importance for climate change mitigation on local and global scales. They are also under considerable threat due to fragmentation degradation and urbanization. However, a complete understanding of how anthropogenic actions can affect microbial biodiversity and functional adaptations is still lacking. In this study, we carried out 16S rRNA gene sequencing analysis using sediment samples from two distinct mangrove areas located within the Serinhaém Estuary, Brazil. The first sampling area was located around the urban area of Ituberá, impacted by domestic sewage and urban runoff, while the second was an environmentally conserved site. Our results show significant changes in the structure of the communities between impacted and conserved sites. Biodiversity, along with functional potentials for the cycling of carbon, nitrogen, phosphorus and sulfur, were significantly increased in the urban area. We found that the environmental factors of organic matter, temperature and copper were significantly correlated with the observed shifts in the communities. Contributions of specific taxa to the functional potentials were negatively correlated with biodiversity, such that fewer numbers of taxa in the conserved area contributed to the majority of the metabolic potential. The results suggest that the contamination by urban runoff may have generated a different environment that led to the extinction of some taxa observed at the conserved site. In their place we found that the impacted site is enriched in prokaryotic families that are known human and animal pathogens, a clear negative effect of the urbanization process.
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Affiliation(s)
| | - Pieter Spealman
- Department of Biology, New York University, New York City, NY, United States of America
| | - Vania Melo
- Department of Biology, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - David Gresham
- Department of Biology, New York University, New York City, NY, United States of America
| | - Taise de Jesus
- Department of Biology, State University of Feira de Santana, Feira de Santana, Bahia, Brazil
| | - Eddy Oliveira
- Department of Biology, State University of Feira de Santana, Feira de Santana, Bahia, Brazil
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8
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Tavares TCL, Bezerra WM, Normando LRO, Rosado AS, Melo VMM. Brazilian Semi-Arid Mangroves-Associated Microbiome as Pools of Richness and Complexity in a Changing World. Front Microbiol 2021; 12:715991. [PMID: 34512595 PMCID: PMC8427804 DOI: 10.3389/fmicb.2021.715991] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 08/06/2021] [Indexed: 01/04/2023] Open
Abstract
Mangrove microbiomes play an essential role in the fate of mangroves in our changing planet, but the factors regulating the biogeographical distribution of mangrove microbial communities remain essentially vague. This paper contributes to our understanding of mangrove microbiomes distributed along three biogeographical provinces and ecoregions, covering the exuberant mangroves of Amazonia ecoregion (North Brazil Shelf) as well as mangroves located in the southern limit of distribution (Southeastern ecoregion, Warm Temperate Southwestern Atlantic) and mangroves localized on the drier semi-arid coast (Northeastern ecoregion, Tropical Southwestern Atlantic), two important ecotones where poleward and landward shifts, respectively, are expected to occur related to climate change. This study compared the microbiomes associated with the conspicuous red mangrove (Rhizophora mangle) root soils encompassing soil properties, latitudinal factors, and amplicon sequence variants of 105 samples. We demonstrated that, although the northern and southern sites are over 4,000 km apart, and despite R. mangle genetic divergences between north and south populations, their microbiomes resemble each other more than the northern and northeastern neighbors. In addition, the northeastern semi-arid microbiomes were more diverse and displayed a higher level of complexity than the northern and southern ones. This finding may reflect the endurance of the northeast microbial communities tailored to deal with the stressful conditions of semi-aridity and may play a role in the resistance and growing landward expansion observed in such mangroves. Minimum temperature, precipitation, organic carbon, and potential evapotranspiration were the main microbiota variation drivers and should be considered in mangrove conservation and recovery strategies in the Anthropocene. In the face of changes in climate, land cover, biodiversity, and chemical composition, the richness and complexity harbored by semi-arid mangrove microbiomes may hold the key to mangrove adaptability in our changing planet.
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Affiliation(s)
| | - Walderly Melgaço Bezerra
- Laboratory of Microbial Ecology and Biotechnology, Department of Biology, Federal University of Ceará (UFC), Fortaleza, Brazil
| | | | - Alexandre Soares Rosado
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Vânia Maria Maciel Melo
- Laboratory of Microbial Ecology and Biotechnology, Department of Biology, Federal University of Ceará (UFC), Fortaleza, Brazil
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9
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Long Y, Jiang J, Hu X, Hu J, Ren C, Zhou S. The response of microbial community structure and sediment properties to anthropogenic activities in Caohai wetland sediments. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 211:111936. [PMID: 33482494 DOI: 10.1016/j.ecoenv.2021.111936] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 01/01/2021] [Accepted: 01/11/2021] [Indexed: 06/12/2023]
Abstract
This study aimed to investigate the response of sediment microbial communities (including bacteria and archaeal groups) in Caohai Lake to anthropogenic activities. The sediment samples were collected from the regions with high anthropogenic interference and low anthropogenic interference. Their physicochemical properties and enzyme activities were analyzed, and the bacterial and archaeal communities were investigated using high-throughput sequencing technology. The results showed that the physicochemical characters changed by anthropogenic activities were the important factors that influenced enzyme activities, alpha diversity, key functional taxa, and community structure. And the impact of anthropogenic activities on microbial communities might follow a non-linear pattern. Furthermore, few significant differences of alpha indices between the high and low disturbed areas, but clear differences of microbial community composition analysis and beta-diversity analysis were observed. The hypothesis was proved that the intensity of anthropogenic impacts in Caohai had not reached the potential thresholds. The best distinguish biomarkers between the two areas and the most related key nodes among the network did not always have a high microbial abundance. The anthropogenic activities might influence the microbial community by affecting a small number of the key taxon in the ecological network. These findings provided a valuable understanding of how sediment microorganisms respond to anthropogenic activities in Caohai Lake.
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Affiliation(s)
- Yunchuan Long
- College of Resource and Environmental Engineering, Guizhou University, Guiyang 550003, PR China; Guizhou Academy of Sciences, Guiyang 550009, PR China
| | - Juan Jiang
- Guizhou Academy of Sciences, Guiyang 550009, PR China
| | - Xuejun Hu
- Guizhou Academy of Sciences, Guiyang 550009, PR China
| | - Jing Hu
- College of Resource and Environmental Engineering, Guizhou University, Guiyang 550003, PR China; Guizhou Academy of Sciences, Guiyang 550009, PR China
| | - Chunguang Ren
- Guizhou Academy of Sciences, Guiyang 550009, PR China
| | - Shaoqi Zhou
- College of Resource and Environmental Engineering, Guizhou University, Guiyang 550003, PR China; Guizhou Academy of Sciences, Guiyang 550009, PR China.
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10
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Wood JR, Burge OR, Bolstridge N, Bonner K, Clarkson B, Cole TL, Davis C, Fergus A, King P, McKeown MM, Morse C, Richardson SJ, Robertson H, Wilmshurst JM. Vertical distribution of prokaryotes communities and predicted metabolic pathways in New Zealand wetlands, and potential for environmental DNA indicators of wetland condition. PLoS One 2021; 16:e0243363. [PMID: 33406114 PMCID: PMC7787371 DOI: 10.1371/journal.pone.0243363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 11/19/2020] [Indexed: 01/04/2023] Open
Abstract
Globally, wetlands are in decline due to anthropogenic modification and climate change. Knowledge about the spatial distribution of biodiversity and biological processes within wetlands provides essential baseline data for predicting and mitigating the effects of present and future environmental change on these critical ecosystems. To explore the potential for environmental DNA (eDNA) to provide such insights, we used 16S rRNA metabarcoding to characterise prokaryote communities and predict the distribution of prokaryote metabolic pathways in peats and sediments up to 4m below the surface across seven New Zealand wetlands. Our results reveal distinct vertical structuring of prokaryote communities and metabolic pathways in these wetlands. We also find evidence for differences in the relative abundance of certain metabolic pathways that may correspond to the degree of anthropogenic modification the wetlands have experienced. These patterns, specifically those for pathways related to aerobic respiration and the carbon cycle, can be explained predominantly by the expected effects of wetland drainage. Our study demonstrates that eDNA has the potential to be an important new tool for the assessment and monitoring of wetland health.
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Affiliation(s)
- Jamie R. Wood
- Manaaki Whenua–Landcare Research, Lincoln, New Zealand
| | | | | | - Karen Bonner
- Manaaki Whenua–Landcare Research, Lincoln, New Zealand
| | | | - Theresa L. Cole
- Department of Biology, Ecology and Evolution, University of Copenhagen, Copenhagen, Denmark
| | - Carina Davis
- Manaaki Whenua–Landcare Research, Lincoln, New Zealand
| | - Alex Fergus
- Manaaki Whenua–Landcare Research, Lincoln, New Zealand
| | - Perēri King
- Maungaharuru-Tangitū Trust, Hawke's Bay Mail Centre, Napier, New Zealand
| | | | - Chris Morse
- Manaaki Whenua–Landcare Research, Lincoln, New Zealand
| | | | | | - Janet M. Wilmshurst
- Manaaki Whenua–Landcare Research, Lincoln, New Zealand
- School of Environment, The University of Auckland, Auckland, New Zealand
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11
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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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12
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Wang B, Zheng X, Zhang H, Xiao F, Gu H, Zhang K, He Z, Liu X, Yan Q. Bacterial community responses to tourism development in the Xixi National Wetland Park, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 720:137570. [PMID: 32135287 DOI: 10.1016/j.scitotenv.2020.137570] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 02/23/2020] [Accepted: 02/24/2020] [Indexed: 06/10/2023]
Abstract
A large number of urban wetland parks have been established, but knowledge about the effects of tourism development on the microbial diversity and ecosystem functioning remains limited. This study aimed to clarify the responses of bacterial communities to tourism development targeted the Xixi National Wetland Park, China. By analyzing the diversity, composition, assembly pattern, and environmental drivers of bacterial communities, we found that tourism development considerably affected the water quality, which further decreased the α-diversity but increased the β-diversity in open areas for landscaping and recreation. Specifically, there was higher Simpson dissimilarity across functional wetland areas, indicating that species replacement mainly explained β-diversity patterns of bacterial communities. RDA analysis and ecological processes quantification further suggested that TOC and TC were the major factors in the open areas driving bacterial communities in water and sediment, respectively. Also, typical anti-disturbance taxa (Gammaproteobacteria) and potential pathogens (Bacillus) were enriched in the wetlands under more anthropogenic disturbances. Findings of the present study highlighted the effects of tourism development on bacterial communities resulted in obvious spatial variation in the Xixi National Wetland Park. This study gives us useful information for ecological assessments of urban wetlands, and further can provide references in making appropriate strategies to manage wetland ecosystems.
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Affiliation(s)
- Binhao Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Xiafei Zheng
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Hangjun Zhang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Fanshu Xiao
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Hang Gu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Keke Zhang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China; College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Xiang Liu
- Hangzhou Xixi National Wetland Park Research Center for Ecological Science, Hangzhou 310030, China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China.
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13
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Mukherji S, Ghosh A, Bhattacharyya C, Mallick I, Bhattacharyya A, Mitra S, Ghosh A. Molecular and culture-based surveys of metabolically active hydrocarbon-degrading archaeal communities in Sundarban mangrove sediments. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 195:110481. [PMID: 32203775 DOI: 10.1016/j.ecoenv.2020.110481] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 02/21/2020] [Accepted: 03/13/2020] [Indexed: 06/10/2023]
Abstract
Archaea remain important players in global biogeochemical cycles worldwide, including in the highly productive mangrove estuarine ecosystems. In the present study, we have explored the diversity, distribution, and function of the metabolically active fraction of the resident archaeal community of the Sundarban mangrove ecosystem, using both culture-independent and culture-dependent approaches. To evaluate the diversity and distribution pattern of the active archaeal communities, RNA based analysis of the 16S rRNA gene was performed on an Illumina platform. The active Crenarchaeal community was observed to remain constant while active Euryarchaeal community underwent considerable change across the sampling sites depending on varying anthropogenic factors. Haloarchaea were the predominant group in hydrocarbon polluted sediments, leading us to successfully isolate eleven p-hydroxybenzoic acid degrading haloarchaeal species. The isolates could also survive in benzoic acid, naphthalene, and o-phthalate. Quantitative estimation of p-hydroxybenzoic acid degradation was studied on select isolates, and their ability to reduce COD of polluted saline waters of Sundarban was also evaluated. To our knowledge, this is the first ever study combining culture-independent (Next Generation sequencing and metatranscriptome) and culture-dependent analyses for an assessment of archaeal function in the sediment of Sundarban.
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Affiliation(s)
- Shayantan Mukherji
- Department of Biochemistry, Bose Institute, P1/12- C.I.T. Road, Scheme VIIM, Kolkata, 700054, West Bengal, India
| | - Anandita Ghosh
- Department of Biochemistry, Bose Institute, P1/12- C.I.T. Road, Scheme VIIM, Kolkata, 700054, West Bengal, India
| | - Chandrima Bhattacharyya
- Department of Biochemistry, Bose Institute, P1/12- C.I.T. Road, Scheme VIIM, Kolkata, 700054, West Bengal, India
| | - Ivy Mallick
- Department of Biochemistry, Bose Institute, P1/12- C.I.T. Road, Scheme VIIM, Kolkata, 700054, West Bengal, India
| | - Anish Bhattacharyya
- Department of Biochemistry, 35 Ballygunge Circular Road, University of Calcutta, Kolkata, 700019, India
| | - Suparna Mitra
- Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, Thoresby Place, Leeds, LS1 3EX, W. Yorkshire, United Kingdom
| | - Abhrajyoti Ghosh
- Department of Biochemistry, Bose Institute, P1/12- C.I.T. Road, Scheme VIIM, Kolkata, 700054, West Bengal, India.
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14
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Wang W, Yi Y, Yang Y, Zhou Y, Jia W, Zhang S, Wang X, Yang Z. Response mechanisms of sediment microbial communities in different habitat types in a shallow lake. Ecosphere 2019. [DOI: 10.1002/ecs2.2948] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Wenjun Wang
- State Key Laboratory of Water Environment Simulation Beijing Normal University Beijing 100875 China
| | - Yujun Yi
- State Key Laboratory of Water Environment Simulation Beijing Normal University Beijing 100875 China
- School of Environment Ministry of Education Key Laboratory of Water and Sediment Science Beijing Normal University Beijing 100875 China
| | - Yufeng Yang
- State Key Laboratory of Water Environment Simulation Beijing Normal University Beijing 100875 China
| | - Yang Zhou
- State Key Laboratory of Water Environment Simulation Beijing Normal University Beijing 100875 China
| | - Wenfei Jia
- State Key Laboratory of Water Environment Simulation Beijing Normal University Beijing 100875 China
| | - Shanghong Zhang
- Renewable Energy School North China Electric Power University Beijing 102206 China
| | - Xuan Wang
- State Key Laboratory of Water Environment Simulation Beijing Normal University Beijing 100875 China
| | - Zhifeng Yang
- State Key Laboratory of Water Environment Simulation Beijing Normal University Beijing 100875 China
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15
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Gong B, Cao H, Peng C, Perčulija V, Tong G, Fang H, Wei X, Ouyang S. High-throughput sequencing and analysis of microbial communities in the mangrove swamps along the coast of Beibu Gulf in Guangxi, China. Sci Rep 2019; 9:9377. [PMID: 31253826 PMCID: PMC6599077 DOI: 10.1038/s41598-019-45804-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 06/13/2019] [Indexed: 02/07/2023] Open
Abstract
Mangrove swamp is one of the world's richest and most productive marine ecosystems. This ecosystem also has a great ecological importance, but is highly susceptible to anthropogenic disturbances. The balance of mangrove ecosystem depends largely on the microbial communities in mangrove sediments. Thus, understanding how the mangrove microbial communities respond to spatial differences is essential for more accurate assessment of mangrove ecosystem health. To this end, we performed the first medium-distance (150 km) research on the biogeographic distribution of mangrove microbial communities. The hypervariable regions of 16S rRNA gene was sequenced by Illumina to compare the microbial communities in mangrove sediments collected from six locations (i.e. Zhenzhu harbor, Yuzhouping, Maowei Sea, Qinzhou harbor, Beihai city and Shankou) along the coastline of Beibu Gulf in Guangxi province, China. Collectively, Proteobacteria, Bacteroidetes, Chloroflexi, Actinobacteria, Parvarchaeota, Acidobacteria and Cyanobacteria were the predominant phyla in the mangrove sediments of this area. At genus level, the heat map of microbial communities reflected similarities between study sites and was in agreement with their biogeographic characteristics. Interestingly, the genera Desulfococcus, Arcobacter, Nitrosopumilus and Sulfurimonas showed differences in abundance between study sites. Furthermore, the principal component analysis (PCA) and unweighted UniFrac cluster tree of beta diversity were used to study the biogeographic diversity of the microbial communities. Relatively broader variation of microbial communities was found in Beihai city and Qinzhou harbour, suggesting that environmental condition and historical events may play an important role in shaping the bacterial communities as well. This is the first report on medium-distance range distribution of bacteria in the mangrove swamp ecosystem. Our data is valuable for monitoring and evaluation of the impact of human activity on mangrove habitats from the perspective of microbiome.
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Affiliation(s)
- Bin Gong
- Guangxi Key Laboratory of Marine Disaster in the Beibu Gulf, Beibu Gulf University, Qinzhou, 535000, China.,The Key Laboratory of Innate Immune Biology of Fujian Province, Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China
| | - Hongming Cao
- Guangxi Key Laboratory of Marine Disaster in the Beibu Gulf, Beibu Gulf University, Qinzhou, 535000, China
| | - Chunyan Peng
- Guangxi Key Laboratory of Marine Disaster in the Beibu Gulf, Beibu Gulf University, Qinzhou, 535000, China
| | - Vanja Perčulija
- The Key Laboratory of Innate Immune Biology of Fujian Province, Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China
| | - Guixiang Tong
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Academy of Fishery Sciences, Nanning, Guangxi, 530021, China
| | - Huaiyi Fang
- Guangxi Key Laboratory of Marine Disaster in the Beibu Gulf, Beibu Gulf University, Qinzhou, 535000, China
| | - Xinxian Wei
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Academy of Fishery Sciences, Nanning, Guangxi, 530021, China.
| | - Songying Ouyang
- The Key Laboratory of Innate Immune Biology of Fujian Province, Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China.
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16
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Tong T, Li R, Wu S, Xie S. The distribution of sediment bacterial community in mangroves across China was governed by geographic location and eutrophication. MARINE POLLUTION BULLETIN 2019; 140:198-203. [PMID: 30803635 DOI: 10.1016/j.marpolbul.2019.01.046] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 01/22/2019] [Accepted: 01/22/2019] [Indexed: 06/09/2023]
Abstract
Bacterial community is an important component of mangrove ecosystem and can participate in the cycling of elements and promote plant growth. However, the biogeographic distribution pattern of mangrove bacterial community and the associated factors remain poorly known. The present study explored the biogeographic distribution of sediment bacterial community in six mangroves across China. At each mangrove, sediments were collected from both Avicennia marina-planted zones and intertidal mudflats. The community abundance, richness, diversity and structure of sediment bacteria differed greatly among mangrove wetlands. Plantation showed a positive influence on sediment bacterial abundance, richness and diversity. Proteobacteria was the largest bacterial phylum in sediments. The biogeographic distribution of bacterial community in mangroves across China was driven by the variables associated with the wetland trophic status as well as other physicochemical factors (e.g., salinity).
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Affiliation(s)
- Tianli Tong
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; School of Environment and Energy, Shenzhen Graduate School of Peking University, Shenzhen 518055, Guangdong, China
| | - Ruili Li
- School of Environment and Energy, Shenzhen Graduate School of Peking University, Shenzhen 518055, Guangdong, China.
| | - Sijie Wu
- School of Environment and Energy, Shenzhen Graduate School of Peking University, Shenzhen 518055, Guangdong, China
| | - Shuguang Xie
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; School of Environment and Energy, Shenzhen Graduate School of Peking University, Shenzhen 518055, Guangdong, China.
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17
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Wiegand S, Jogler M, Jogler C. On the maverick Planctomycetes. FEMS Microbiol Rev 2018; 42:739-760. [DOI: 10.1093/femsre/fuy029] [Citation(s) in RCA: 134] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 07/22/2018] [Indexed: 01/01/2023] Open
Affiliation(s)
- Sandra Wiegand
- Department of Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen, The Netherlands
| | - Mareike Jogler
- Leibniz Institute DSMZ, Inhoffenstraße 7b, 38124 Braunschweig, Germany
| | - Christian Jogler
- Department of Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen, The Netherlands
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