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de Carvalho FM, Laux M, Ciapina LP, Gerber AL, Guimarães APC, Kloh VP, Apolinário M, Paes JES, Jonck CR, de Vasconcelos ATR. Finding microbial composition and biological processes as predictive signature to access the ongoing status of mangrove preservation. Int Microbiol 2024; 27:1485-1500. [PMID: 38388811 PMCID: PMC11452435 DOI: 10.1007/s10123-024-00492-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 01/08/2024] [Accepted: 02/13/2024] [Indexed: 02/24/2024]
Abstract
Mangroves are complex land-sea transition ecosystems whose microbiota are essential for their nutrient recycling and conservation. Brazil is the third-largest estuarine area in the world and "Baía de Todos os Santos" (BTS) is one of the largest bays of the country, with wide anthropogenic exploration. Using a metagenomic approach, we investigated composition and functional adaptability as signatures of the microbiome of pristine and anthropized areas of BTS, including those under petroleum refinery influence. The taxonomic analysis showed dominance of sulfate-reducing Desulfobacteraceae, Rhodobacteraceae, and Flavobacteriaceae. Taxa were significantly diverse between pristine and disturbed areas. Disturbed mangroves showed a notary increase in abundance of halophilic, sulfur-related, and hydrocarbon-degrading genera and a decrease in diatoms compared to pristine area. The metabolic profile of BTS mangroves was correlated with the differentially abundant microbiota. Two ecological scenarios were observed: one marked by functions of central metabolism associated with biomass degradation and another by mechanisms of microbial adaptability to pollution conditions and environmental degradation. Part of the microbiome was distinct and not abundant in Brazilian estuarine soils. The microbiome signature observed in each BTS mangrove reflects how human actions impact the diversity of these ecosystems and also emphasize their role in attempting to restore disturbed mangroves. The microbiome may act as a potential biological indicator of the preservation status of these soils, despite the limitation of soil property conditions. Additionally, our data pointed to metagenomics as an additional tool for environmental assessment and reinforced the need for protective measures for the mangroves under study.
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Affiliation(s)
- Fabíola Marques de Carvalho
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Avenida Getúlio Vargas 333, Quitandinha Petrópolis, Rio de Janeiro, 25651-075, Brazil
| | - Marcele Laux
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Avenida Getúlio Vargas 333, Quitandinha Petrópolis, Rio de Janeiro, 25651-075, Brazil
| | - Luciane Prioli Ciapina
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Avenida Getúlio Vargas 333, Quitandinha Petrópolis, Rio de Janeiro, 25651-075, Brazil
| | - Alexandra Lehmkuhl Gerber
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Avenida Getúlio Vargas 333, Quitandinha Petrópolis, Rio de Janeiro, 25651-075, Brazil
| | - Ana Paula C Guimarães
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Avenida Getúlio Vargas 333, Quitandinha Petrópolis, Rio de Janeiro, 25651-075, Brazil
| | - Vinícius Prata Kloh
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Avenida Getúlio Vargas 333, Quitandinha Petrópolis, Rio de Janeiro, 25651-075, Brazil
| | - Moacir Apolinário
- Petróleo Brasileiro S. A., Centro de Pesquisa Leopoldo Américo Miguez de Mello, Rio de Janeiro, RJ, Brazil
| | - Jorge Eduardo Santos Paes
- Petróleo Brasileiro S. A., Centro de Pesquisa Leopoldo Américo Miguez de Mello, Rio de Janeiro, RJ, Brazil
| | - Célio Roberto Jonck
- Petróleo Brasileiro S. A., Centro de Pesquisa Leopoldo Américo Miguez de Mello, Rio de Janeiro, RJ, Brazil
| | - Ana Tereza R de Vasconcelos
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Avenida Getúlio Vargas 333, Quitandinha Petrópolis, Rio de Janeiro, 25651-075, Brazil.
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Zhang J, Chen J, Wang C, Wang P, Gao H, Feng B, Fu J. Vertical variation of antibiotic resistance genes and their interaction with environmental nutrients in sediments of Taihu lake. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 370:122661. [PMID: 39332305 DOI: 10.1016/j.jenvman.2024.122661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 09/22/2024] [Accepted: 09/23/2024] [Indexed: 09/29/2024]
Abstract
Antibiotic resistance is a growing environmental issue. As a sink for antibiotic resistance genes (ARGs), lake surface sediments are well known for the spread of ARGs. However, the distribution pattern of ARGs and their relationship with environmental factors in vertical sediment layers are unclear. In this study, we investigated the resistome distribution in sediment cores from Taihu Lake using metagenomic analysis. The results showed that the abundance of total ARGs increased by 153% as the sediment depth rose from 0 to 50 cm, and the ARG Shannon index significantly increased. Among all the ARG types, efflux pump genes (e.g., mexT and mexW) were dominant, especially in 40-50 cm sediment. The variation in ARG with depth described above was related to the changes in bacterial adaptation to environmental gradients. Specifically, sulfate and nitrate concentrations decreased with depth, and random forest analysis showed that they were the main factors affecting the changes in ARG abundance. Environmental factors were also found to indirectly impact the distribution of ARGs by affecting the bacterial community. Potential sulfate-reducing gene/nitrate-reducing gene-ARG co-hosts were annotated through metagenomic assembly. The dominant co-hosts, Curvibacter, and Comamonas, which were enriched in deeper sediments, may have contributed to the enrichment of ARGs in deep sediments. Overall, our findings demonstrated that bacterial-mediated sulfate and nitrate reduction was closely related to sediment resistance, which provided new insights into the control of antibiotic resistance.
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Affiliation(s)
- Jingjing Zhang
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing, 210098, PR China
| | - Juan Chen
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing, 210098, PR China.
| | - Chao Wang
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing, 210098, PR China
| | - Peifang Wang
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing, 210098, PR China
| | - Han Gao
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing, 210098, PR China
| | - Bingbing Feng
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing, 210098, PR China
| | - Jingjing Fu
- PowerChina Huadong Engineering Corporation Limited, No.201, Gaojiao Road, Yuhang District, Hangzhou, Zhejiang, 311122, PR China
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Andreani-Gerard CM, Cambiazo V, González M. Biosynthetic gene clusters from uncultivated soil bacteria of the Atacama Desert. mSphere 2024:e0019224. [PMID: 39287428 DOI: 10.1128/msphere.00192-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 08/15/2024] [Indexed: 09/19/2024] Open
Abstract
Soil microorganisms mediate several biological processes through the secretion of natural products synthesized in specialized metabolic pathways, yet functional characterization in ecological contexts remains challenging. Using culture-independent metagenomic analyses of microbial DNA derived directly from soil samples, we examined the potential of biosynthetic gene clusters (BGCs) from six bacterial communities distributed along an altitudinal gradient of the Andes Mountains in the Atacama Desert. We mined 38 metagenome-assembled genomes (MAGs) and identified 168 BGCs. Results indicated that most predicted BGCs were classified as non-ribosomal-peptides (NRP), post-translational modified peptides (RiPP), and terpenes, which were mainly identified in genomes of species from Acidobacteriota and Proteobacteria phyla. Based on BGC composition according to types of core biosynthetic genes, six clusters of MAGs were observed, three of them with predominance for a single phylum, of which two also showed specificity to a single sampling site. Comparative analyses of accessory genes in BGCs showed associations between membrane transporters and other protein domains involved in specialized metabolism with classes of biosynthetic cores, such as resistance-nodulation-cell division (RND) multidrug efflux pumps with RiPPs and the iron-dependent transporter TonB with terpenes. Our findings increase knowledge regarding the biosynthetic potential of uncultured bacteria inhabiting pristine locations from one of the oldest and driest nonpolar deserts on Earth.IMPORTANCEMuch of what we know about specialized metabolites in the Atacama Desert, including Andean ecosystems, comes from isolated microorganisms intended for drug development and natural product discovery. To complement research on the metabolic potential of microbes in extreme environments, comparative analyses on functional annotations of biosynthetic gene clusters (BGCs) from uncultivated bacterial genomes were carried out. Results indicated that in general, BGCs encode for structurally unique metabolites and that metagenome-assembled genomes did not show an obvious relationship between the composition of their core biosynthetic potential and taxonomy or geographic distribution. Nevertheless, some members of Acidobacteriota showed a phylogenetic relationship with specific metabolic traits and a few members of Proteobacteria and Desulfobacterota exhibited niche adaptations. Our results emphasize that studying specialized metabolism in environmental samples may significantly contribute to the elucidation of structures, activities, and ecological roles of microbial molecules.
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Affiliation(s)
- Constanza M Andreani-Gerard
- Millennium Institute Center for Genome Regulation (CRG)
- Bioinformatic and Gene Expression Laboratory, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Santiago, Chile
- Center for Mathematical Modeling (CMM) - Universidad de Chile, Santiago, Chile
| | - Verónica Cambiazo
- Millennium Institute Center for Genome Regulation (CRG)
- Bioinformatic and Gene Expression Laboratory, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Santiago, Chile
| | - Mauricio González
- Millennium Institute Center for Genome Regulation (CRG)
- Bioinformatic and Gene Expression Laboratory, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Santiago, Chile
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Chen J, Jia Y, Sun Y, Liu K, Zhou C, Liu C, Li D, Liu G, Zhang C, Yang T, Huang L, Zhuang Y, Wang D, Xu D, Zhong Q, Guo Y, Li A, Seim I, Jiang L, Wang L, Lee SMY, Liu Y, Wang D, Zhang G, Liu S, Wei X, Yue Z, Zheng S, Shen X, Wang S, Qi C, Chen J, Ye C, Zhao F, Wang J, Fan J, Li B, Sun J, Jia X, Xia Z, Zhang H, Liu J, Zheng Y, Liu X, Wang J, Yang H, Kristiansen K, Xu X, Mock T, Li S, Zhang W, Fan G. Global marine microbial diversity and its potential in bioprospecting. Nature 2024; 633:371-379. [PMID: 39232160 PMCID: PMC11390488 DOI: 10.1038/s41586-024-07891-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 07/31/2024] [Indexed: 09/06/2024]
Abstract
The past two decades has witnessed a remarkable increase in the number of microbial genomes retrieved from marine systems1,2. However, it has remained challenging to translate this marine genomic diversity into biotechnological and biomedical applications3,4. Here we recovered 43,191 bacterial and archaeal genomes from publicly available marine metagenomes, encompassing a wide range of diversity with 138 distinct phyla, redefining the upper limit of marine bacterial genome size and revealing complex trade-offs between the occurrence of CRISPR-Cas systems and antibiotic resistance genes. In silico bioprospecting of these marine genomes led to the discovery of a novel CRISPR-Cas9 system, ten antimicrobial peptides, and three enzymes that degrade polyethylene terephthalate. In vitro experiments confirmed their effectiveness and efficacy. This work provides evidence that global-scale sequencing initiatives advance our understanding of how microbial diversity has evolved in the oceans and is maintained, and demonstrates how such initiatives can be sustainably exploited to advance biotechnology and biomedicine.
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Affiliation(s)
- Jianwei Chen
- BGI Research, Qingdao, China
- BGI Research, Shenzhen, China
- Qingdao Key Laboratory of Marine Genomics and Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Ying Sun
- BGI Research, Qingdao, China.
- Qingdao Key Laboratory of Marine Genomics and Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, China.
| | - Kun Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | | | - Chuan Liu
- BGI Research, Shenzhen, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Chengsong Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Tao Yang
- China National GeneBank, BGI Research, Shenzhen, China
- Guangdong Genomics Data Center, BGI Research, Shenzhen, China
| | | | - Yunyun Zhuang
- Key Laboratory of Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao, China
| | - Dazhi Wang
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | | | | | - Yang Guo
- BGI Research, Qingdao, China
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | | | - Inge Seim
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Ling Jiang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Simon Ming Yuen Lee
- Department of Food Science and Nutrition, and PolyU-BGI Joint Research Centre for Genomics and Synthetic Biology in Global Deep Ocean Resource, The Hong Kong Polytechnic University, Hong Kong, China
| | - Yujing Liu
- BGI Research, Qingdao, China
- Qingdao Key Laboratory of Marine Genomics and Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, China
| | | | - Guoqiang Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | | | - Xiaofeng Wei
- China National GeneBank, BGI Research, Shenzhen, China
- Guangdong Genomics Data Center, BGI Research, Shenzhen, China
| | | | - Shanmin Zheng
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | | | - Sen Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Chen Qi
- BGI Research, Shenzhen, China
| | - Jing Chen
- Guangdong Genomics Data Center, BGI Research, Shenzhen, China
| | - Chen Ye
- BGI Research, Shenzhen, China
| | | | | | - Jie Fan
- BGI Research, Qingdao, China
- Qingdao Key Laboratory of Marine Genomics and Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, China
| | | | | | - Xiaodong Jia
- Joint Laboratory for Translational Medicine Research, Liaocheng People's Hospital, Liaocheng, China
| | - Zhangyong Xia
- Department of Neurology, The Second People's Hospital of Liaocheng, Liaocheng, China
| | - He Zhang
- BGI Research, Qingdao, China
- BGI Research, Shenzhen, China
| | | | | | - Xin Liu
- BGI Research, Qingdao, China
- BGI Research, Shenzhen, China
| | | | | | - Karsten Kristiansen
- BGI Research, Shenzhen, China
- Qingdao Key Laboratory of Marine Genomics and Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Xun Xu
- BGI Research, Qingdao, China
- BGI Research, Shenzhen, China
- Qingdao Key Laboratory of Marine Genomics and Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, China
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, China
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK.
| | - Shengying Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China.
| | - Wenwei Zhang
- BGI Research, Shenzhen, China.
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, China.
| | - Guangyi Fan
- BGI Research, Qingdao, China.
- BGI Research, Shenzhen, China.
- Qingdao Key Laboratory of Marine Genomics and Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, China.
- Department of Food Science and Nutrition, and PolyU-BGI Joint Research Centre for Genomics and Synthetic Biology in Global Deep Ocean Resource, The Hong Kong Polytechnic University, Hong Kong, China.
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, China.
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Chen J, Peng L, Zhou C, Li L, Ge Q, Shi C, Guo W, Guo T, Jiang L, Zhang Z, Fan G, Zhang W, Kristiansen K, Jia Y. Datasets of fungal diversity and pseudo-chromosomal genomes of mangrove rhizosphere soil in China. Sci Data 2024; 11:901. [PMID: 39164251 PMCID: PMC11336097 DOI: 10.1038/s41597-024-03748-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 08/06/2024] [Indexed: 08/22/2024] Open
Abstract
With climate change and anthropic influence on the coastal ecosystems, mangrove ecosystems are disappearing at an alarming rate. Accordingly, it becomes important to track, study, record and store the mangrove microbial community considering their ecological importance and potential for biotechnological applications. Here, we provide information on mangrove fungal community composition and diversity in mangrove ecosystems with different plant species and from various locations differing in relation to anthropic influences. We describe twelve newly assembled genomes, including four chromosomal-level genomes of fungal isolates from the mangrove ecosystems coupled with functional annotations. We envisage that these data will be of value for future studies including comparative genome analysis and large-scale temporal and/or spatial research to elucidate the potential mechanisms by which mangrove fungal communities assemble and evolve. We further anticipate that the genomes represent valuable resources for bioprospecting related to industrial or clinical uses.
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Affiliation(s)
- Jianwei Chen
- BGI Research, Qingdao, 266555, China
- Qingdao Key Laboratory of Marine Genomics, and Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, 266555, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Universitetsparken 13, 2100, Copenhagen, Denmark
| | - Ling Peng
- BGI Research, Qingdao, 266555, China
| | - Changhao Zhou
- BGI Research, Qingdao, 266555, China
- Qingdao Key Laboratory of Marine Genomics, and Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, 266555, China
| | | | - Qijin Ge
- BGI Research, Qingdao, 266555, China
| | | | | | | | - Ling Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Zhidong Zhang
- Xinjiang Key Laboratory of Special Environmental Microbiology, Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, China
| | - Guangyi Fan
- BGI Research, Qingdao, 266555, China
- Qingdao Key Laboratory of Marine Genomics, and Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, 266555, China
- BGI Research, Shenzhen, 518083, China
| | | | - Karsten Kristiansen
- Qingdao Key Laboratory of Marine Genomics, and Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, 266555, China.
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Universitetsparken 13, 2100, Copenhagen, Denmark.
- BGI Research, Shenzhen, 518083, China.
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Esguerra-Rodríguez D, De León-Lorenzana A, Teutli C, Prieto-Davó A, García-Maldonado JQ, Herrera-Silveira J, Falcón LI. Do restoration strategies in mangroves recover microbial diversity? A case study in the Yucatan peninsula. PLoS One 2024; 19:e0307929. [PMID: 39150908 PMCID: PMC11329136 DOI: 10.1371/journal.pone.0307929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 07/15/2024] [Indexed: 08/18/2024] Open
Abstract
Mangrove forests are fundamental coastal ecosystems for the variety of services they provide, including green-house gas regulation, coastal protection and home to a great biodiversity. Mexico is the fourth country with the largest extension of mangroves of which 60% occurs in the Yucatan Peninsula. Understanding the microbial component of mangrove forests is necessary for their critical roles in biogeochemical cycles, ecosystem health, function and restoration initiatives. Here we study the relation between the microbial community from sediments and the restoration process of mangrove forests, comparing conserved, degraded and restored mangroves along the northern coast of the Yucatan peninsula. Results showed that although each sampling site had a differentiated microbial composition, the taxa belonged predominantly to Proteobacteria (13.2-23.6%), Desulfobacterota (7.6-8.3%) and Chloroflexi (9-15.7%) phyla, and these were similar between rainy and dry seasons. Conserved mangroves showed significantly higher diversity than degraded ones, and restored mangroves recovered their microbial diversity from the degraded state (Dunn test p-value Benjamini-Hochberg adjusted = 0.0034 and 0.0071 respectively). The structure of sediment microbial β-diversity responded significantly to the mangrove conservation status and physicochemical parameters (organic carbon content, redox potential, and salinity). Taxa within Chloroflexota, Desulfobacterota and Thermoplasmatota showed significantly higher abundance in degraded mangrove samples compared to conserved ones. This study can help set a baseline that includes the microbial component in health assessment and restoration strategies of mangrove forests.
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Affiliation(s)
- Daniel Esguerra-Rodríguez
- Posgrado en Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Ciudad de México, México
- Instituto de Ecología, Laboratorio de Ecología Bacteriana, Unidad Mérida, Ucú, Yucatán, México
| | - Arit De León-Lorenzana
- Instituto de Ecología, Laboratorio de Ecología Bacteriana, Unidad Mérida, Ucú, Yucatán, México
| | - Claudia Teutli
- Escuela Nacional de Estudios Superiores Mérida, Universidad Nacional Autónoma de México, Ucú, Yucatán, México
| | - Alejandra Prieto-Davó
- Facultad de Química, Unidad de Química Sisal, Universidad Nacional Autónoma de México, Sisal, Yucatán, México
| | - José Q García-Maldonado
- Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán, México
| | - Jorge Herrera-Silveira
- Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán, México
| | - Luisa I Falcón
- Instituto de Ecología, Laboratorio de Ecología Bacteriana, Unidad Mérida, Ucú, Yucatán, México
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7
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Bushra R, Ahmed I, Li JL, Lian Z, Li S, Ali A, Uzair B, Amin A, Ehsan M, Liu YH, Li WJ. Untapped rich microbiota of mangroves of Pakistan: diversity and community compositions. Folia Microbiol (Praha) 2024; 69:595-612. [PMID: 37843797 DOI: 10.1007/s12223-023-01095-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 09/11/2023] [Indexed: 10/17/2023]
Abstract
The mangrove ecosystem is the world's fourth most productive ecosystem in terms of service value and offering rich biological resources. Microorganisms play vital roles in these ecological processes, thus researching the mangroves-microbiota is crucial for a deeper comprehension of mangroves dynamics. Amplicon sequencing that targeted V4 region of 16S rRNA gene was employed to profile the microbial diversities and community compositions of 19 soil samples, which were collected from the rhizosphere of 3 plant species (i.e., Avicennia marina, Ceriops tagal, and Rhizophora mucronata) in the mangrove forests of Lasbela coast, Pakistan. A total of 67 bacterial phyla were observed from three mangroves species, and these taxa were classified into 188 classes, 453 orders, 759 families, and 1327 genera. We found that Proteobacteria (34.9-38.4%) and Desulfobacteria (7.6-10.0%) were the dominant phyla followed by Chloroflexi (6.6-7.3%), Gemmatimonadota (5.4-6.8%), Bacteroidota (4.3-5.5%), Planctomycetota (4.4-4.9%) and Acidobacteriota (2.7-3.4%), Actinobacteriota (2.5-3.3%), and Crenarchaeota (2.5-3.3%). After considering the distribution of taxonomic groups, we prescribe that the distinctions in bacterial community composition and diversity are ascribed to the changes in physicochemical attributes of the soil samples (i.e., electrical conductivity (ECe), pH, total organic matter (OM), total organic carbon (OC), available phosphorus (P), and extractable potassium (CaCO3). The findings of this study indicated a high-level species diversity in Pakistani mangroves. The outcomes may also aid in the development of effective conservation policies for mangrove ecosystems, which have been hotspots for anthropogenic impacts in Pakistan. To our knowledge, this is the first microbial research from a Pakistani mangrove forest.
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Affiliation(s)
- Rabia Bushra
- National Culture Collection of Pakistan (NCCP), Land Resources Research Institute (LRRI), National Agriculture Research Center (NARC), Islamabad 45500, Pakistan
- Department of Biological Sciences, International Islamic University, Islamabad 44000, Pakistan
| | - Iftikhar Ahmed
- National Culture Collection of Pakistan (NCCP), Land Resources Research Institute (LRRI), National Agriculture Research Center (NARC), Islamabad 45500, Pakistan.
| | - Jia-Ling Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Zhenghan Lian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Shuai Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Ahmad Ali
- National Culture Collection of Pakistan (NCCP), Land Resources Research Institute (LRRI), National Agriculture Research Center (NARC), Islamabad 45500, Pakistan
| | - Bushra Uzair
- Department of Biological Sciences, International Islamic University, Islamabad 44000, Pakistan
| | - Arshia Amin
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad 45500, Pakistan
| | | | - Yong-Hong Liu
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China.
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8
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Zhang M, Xiong J, Zhou L, Li J, Fan J, Li X, Zhang T, Yin Z, Yin H, Liu X, Meng D. Community ecological study on the reduction of soil antimony bioavailability by SRB-based remediation technologies. JOURNAL OF HAZARDOUS MATERIALS 2023; 459:132256. [PMID: 37567138 DOI: 10.1016/j.jhazmat.2023.132256] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 07/27/2023] [Accepted: 08/07/2023] [Indexed: 08/13/2023]
Abstract
Sulfate-reducing bacteria (SRB) were effective in stabilizing Sb. However, the influence of electron donors and acceptors during SRB remediation, as well as the ecological principles involved, remained unclear. In this study, Desulfovibrio desulfuricans ATCC 7757 was utilized to stabilize soil Sb within microcosm. Humic acid (HA) or sodium sulfate (Na2SO4) were employed to enhance SRB capacity. The SRB+HA treatment exhibited the highest Sb stabilization rate, achieving 58.40%. Bacterial community analysis revealed that SRB altered soil bacterial diversity, community composition, and assembly processes, with homogeneous selection as the predominant assembly processes. When HA and Na2SO4 significantly modified the stimulated microbial community succession trajectories, shaped the taxonomic composition and interactions of the bacterial community, they showed converse effect in shaping bacterial community which were both helpful for promoting dissimilatory sulfate reduction. Na2SO4 facilitated SRB-mediated anaerobic reduction and promoted interactions between SRB and bacteria involved in nitrogen and sulfur cycling. The HA stimulated electron generation and storage, and enhanced the interactions between SRB and bacteria possessing heavy metal tolerance or carbohydrate degradation capabilities.
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Affiliation(s)
- Min Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; Key laboratory of Biometallurgy, Ministry of Education, Changsha 410083, China
| | - Jing Xiong
- Hunan urban and Rural Environmental Construction Co., Ltd, Changsha 410118, China
| | - Lei Zhou
- Beijing Research Institute of Chemical Engineering and Metallurgy, Beijing 101148, China
| | - Jingjing Li
- Technology Center, China Tobacco Fujian Industrial Co., Ltd., Xiamen, Fujian 361000, China
| | - Jianqiang Fan
- Technology Center, China Tobacco Fujian Industrial Co., Ltd., Xiamen, Fujian 361000, China
| | - Xing Li
- Hunan HIKEE Environmental Technology CO., LTD, Changsha 410221, China
| | - Teng Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; Hunan urban and Rural Environmental Construction Co., Ltd, Changsha 410118, China; Key laboratory of Biometallurgy, Ministry of Education, Changsha 410083, China
| | - Zhuzhong Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; Key laboratory of Biometallurgy, Ministry of Education, Changsha 410083, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; Key laboratory of Biometallurgy, Ministry of Education, Changsha 410083, China
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; Key laboratory of Biometallurgy, Ministry of Education, Changsha 410083, China
| | - Delong Meng
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; Key laboratory of Biometallurgy, Ministry of Education, Changsha 410083, China.
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Du H, Pan J, Zhang C, Yang X, Wang C, Lin X, Li J, Liu W, Zhou H, Yu X, Mo S, Zhang G, Zhao G, Qu W, Jiang C, Tian Y, He Z, Liu Y, Li M. Analogous assembly mechanisms and functional guilds govern prokaryotic communities in mangrove ecosystems of China and South America. Microbiol Spectr 2023; 11:e0157723. [PMID: 37668400 PMCID: PMC10580968 DOI: 10.1128/spectrum.01577-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 07/19/2023] [Indexed: 09/06/2023] Open
Abstract
As an important coastal "blue carbon sink," mangrove ecosystems contain microbial communities with an as-yet-unknown high species diversity. Exploring the assemblage and structure of sediment microbial communities therein can aid in a better understanding of their ecosystem functioning, such as carbon sequestration and other biogeochemical cycles in mangrove wetlands. However, compared to other biomes, the study of mangrove sediment microbiomes is limited, especially in diverse mangrove ecosystems at a large spatial scale, which may harbor microbial communities with distinct compositions and functioning. Here, we analyzed 380 sediment samples from 13 and 8 representative mangrove ecosystems, respectively, in China and South America and compared their microbial features. Although the microbial community compositions exhibited strong distinctions, the community assemblage in the two locations followed analogous patterns: the assemblages of the entire community, abundant taxa, rare taxa, and generalists were predominantly driven by stochastic processes with significant distance-decay patterns, while the assembly of specialists was more likely related to the behaviors of other organisms in or surrounding the mangrove ecosystems. In addition, co-occurrence and topological network analysis of mangrove sediment microbiomes underlined the dominance of sulfate-reducing prokaryotes in both the regions. Moreover, we found that more than 70% of the keystone and hub taxa were sulfate-reducing prokaryotes, implying their important roles in maintaining the linkage and stability of the mangrove sediment microbial communities. This study fills a gap in the large-scale analysis of microbiome features covering distantly located and diverse mangrove ecosystems. Here, we propose a suggestion to the Mangrove Microbiome Initiative that 16S rRNA sequencing protocols should be standardized with a unified primer to facilitate the global-scale analysis of mangrove microbiomes and further comparisons with the reference data sets from other biomes.IMPORTANCEMangrove wetlands are important ecosystems possessing valuable ecological functions for carbon storage, species diversity maintenance, and coastline stabilization. These functions are greatly driven or supported by microorganisms that make essential contributions to biogeochemical cycles in mangrove ecosystems. The mechanisms governing the microbial community assembly, structure, and functions are vital to microbial ecology but remain unclear. Moreover, studying these mechanisms of mangrove microbiomes at a large spatial scale can provide a more comprehensive insight into their universal features and can help untangle microbial interaction patterns and microbiome functions. In this study, we compared the mangrove microbiomes in a large spatial range and found that the assembly patterns and key functional guilds of the Chinese and South American mangrove microbiomes were analogous. The entire communities exhibited significant distance-decay patterns and were strongly governed by stochastic processes, while the assemblage of specialists may be merely associated with the behaviors of the organisms in mangrove ecosystems. Furthermore, our results highlight the dominance of sulfate-reducing prokaryotes in mangrove microbiomes and their key roles in maintaining the stability of community structure and functions.
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Affiliation(s)
- Huan Du
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Jie Pan
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Shenzhen Xbiome Biotech Co. Ltd., Shenzhen, China
| | - Cuijing Zhang
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Xilan Yang
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen, China
- Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Cheng Wang
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
- State Key Laboratory for Biocontrol, Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China
| | - Xiaolan Lin
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, China
| | - Jinhui Li
- National Engineering Research Center for Non-Food Biorefinery, Guangxi Research Center for Biological Science and Technology, Guangxi Academy of Sciences, Nanning, China
| | - Wan Liu
- National Genomics Data Center& Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Science, Shanghai, China
| | - Haokui Zhou
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen, China
- Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Xiaoli Yu
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
- State Key Laboratory for Biocontrol, Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China
| | - Shuming Mo
- National Engineering Research Center for Non-Food Biorefinery, Guangxi Research Center for Biological Science and Technology, Guangxi Academy of Sciences, Nanning, China
| | - Guoqing Zhang
- National Genomics Data Center& Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Science, Shanghai, China
| | - Guoping Zhao
- National Genomics Data Center& Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Science, Shanghai, China
- Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Wu Qu
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, China
| | - Chengjian Jiang
- National Engineering Research Center for Non-Food Biorefinery, Guangxi Research Center for Biological Science and Technology, Guangxi Academy of Sciences, Nanning, China
| | - Yun Tian
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, China
| | - Zhili He
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
- State Key Laboratory for Biocontrol, Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China
| | - Yang Liu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
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10
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Wilfred G, Songoro EK, Gathirwa JW, Kimani F, Kariuki HN. In vivo antiplasmodial activities of stem bark extracts of Avicennia marina in Plasmodium berghei-infected mice. Pan Afr Med J 2023; 44:93. [PMID: 37229304 PMCID: PMC10204109 DOI: 10.11604/pamj.2023.44.93.38448] [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: 12/06/2022] [Accepted: 01/13/2023] [Indexed: 05/27/2023] Open
Abstract
Introduction malaria remains the leading cause of morbidity and mortality in developing tropical and subtropical nations. Due to the emergence and spread of drug resistance to currently available drugs, there is a need for the search of novel, safe, and reasonably affordable anti-malarial medications. The objective of this study was to assess the in vivoanti-malarial effectiveness of Avicennia marina stem bark extracts in a mice model. Methods guidelines 425 of the Organization for Economic Cooperation and Development were used to determine the extracts' acute toxicity. Mice infected with chloroquine-sensitive Plasmodium berghei (ANKA strain) were tested for in vivoanti-plasmodial activity, and by giving oral doses of 100 mg/kg, 250 mg/kg, and 500 mg/kg body weight of extracts, the plant's suppressive, curative, and preventive effects were assessed. Results mice treated with dosages of up to 5000 mg/kg showed no evidence of acute toxicity or mortality. Consequently, it was determined that the acute lethal dosage of Avicennia marina extracts in swiss albino mice was greater than 5000 mg/kg. All doses of the extracts exhibited significant (p<0.05) dose-dependent suppression of P. berghei in the suppressive tests compared to the control group. At the highest dose (500 mg/kg), Methanolic crude extracts exerted the highest (93%) parasitemia suppression during the 4-day suppressive test. The extracts also displayed significant (p<0.001) prophylactic and curative activities at all doses compared to the control. Conclusion results from this study ascertained the safety and promising curative, prophylactic and suppressive anti-plasmodial capabilities of the stem bark extracts of Avicennia marina in mice model.
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Affiliation(s)
- Gitau Wilfred
- Department of Medical Microbiology, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Edinah Kwamboka Songoro
- Department of Medical Microbiology, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Jeremiah Waweru Gathirwa
- Centre for Traditional Medicine, Drugs and Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Francis Kimani
- Centre for Biotechnology, Research Development, Kenya Medical Research Institute, Nairobi, Kenya
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11
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Isolation and Genomics of Futiania mangrovii gen. nov., sp. nov., a Rare and Metabolically Versatile Member in the Class Alphaproteobacteria. Microbiol Spectr 2023; 11:e0411022. [PMID: 36541777 PMCID: PMC9927469 DOI: 10.1128/spectrum.04110-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Mangrove microorganisms are a major part of the coastal ecosystem and are directly associated with nutrient cycling. Despite their ecological significance, the collection of culturable mangrove microbes is limited due to difficulties in isolation and cultivation. Here, we report the isolation and genome sequence of strain FT118T, the first cultured representative of a previously uncultivated order UBA8317 within Alphaproteobacteria, based on the combined results of 16S rRNA gene similarity, phylogenomic, and average amino acid identity analyses. We propose Futianiales ord. nov. and Futianiaceae fam. nov. with Futiania as the type genus, and FT118T represents the type species with the name Futiania mangrovii gen. nov, sp. nov. The 16S rRNA gene sequence comparison reveals that this novel order is a rare member but has a ubiquitous distribution across various habitats worldwide, which is corroborated by the experimental confirmation that this isolate can physiologically adapt to a wide range of oxygen levels, temperatures, pH and salinity levels. Biochemical characterization, genomic annotation, and metatranscriptomic analysis of FT118T demonstrate that it is metabolically versatile and active in situ. Genomic analysis reveals adaptive features of Futianiales to fluctuating mangrove environments, including the presence of high- and low-affinity terminal oxidases, N-type ATPase, and the genomic capability of producing various compatible solutes and polyhydroxybutyrate, which possibly allow for the persistence of this novel order across various habitats. Collectively, these results expand the current culture collection of mangrove microorganisms, providing genomic insights of how this novel taxon adapts to fluctuating environments and the culture reference to unravel possible microbe-environment interactions. IMPORTANCE The rare biosphere constitutes an essential part of the microbial community and may drive nutrient cycling and other geochemical processes. However, the difficulty in microbial isolation and cultivation has hampered our understanding of the physiology and ecology of uncultured rare lineages. In this study, we successfully isolated a novel alphaproteobacterium, designated as FT118T, and performed a combination of phenotypic, phylogenetic, and phylogenomic analyses, confirming that this isolate represents the first cultured member of a previously uncultivated order UBA8317 within Alphaproteobacteria. It is a rare species with a ubiquitous distribution across different habitats. Genomic and metatranscriptomic analyses demonstrate that it is metabolically versatile and active in situ, suggesting its potential role in nutrient cycling despite being scarce. This work not only expands the current phylogeny of isolated Alphaproteobacteria but also provides genomic and culture reference to unravel microbial adaptation strategies in mangrove sediments and possible microbe-environment interactions.
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12
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Wu Y, Jiang B, Zou Y, Dong H, Wang H, Zou H. Influence of bacterial community diversity, functionality, and soil factors on polycyclic aromatic hydrocarbons under various vegetation types in mangrove wetlands. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 308:119622. [PMID: 35750309 DOI: 10.1016/j.envpol.2022.119622] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 05/04/2022] [Accepted: 06/12/2022] [Indexed: 06/15/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are prevalent organic pollutants in coastal ecosystems, particularly in mangrove wetlands. However, it is still largely unclear how PAHs affect the soil bacterial community under various vegetation types in the Greater Bay Area. Here, we selected soil samples from four sites with different vegetation types (native mangrove forest dominated by Kandelia candel, invasive mangrove forest dominated by Sonneratia apetala, unvegetated mudflat, and riverine runoff outlet) in the Qi'ao and Futian Nature Reserves. We investigated the effects of PAHs on soil bacterial community composition and diversity, function, and co-occurrence via 16S rRNA high-throughput sequencing. PAHs obviously reduced soil bacterial community diversity and richness. Based on PICRUSt 2, PAHs demonstrated positive influences on PAHs degradation metabolism related bacterial genes. Meanwhile, we predicted that riverine runoff outlets can potentially degrade PAHs, may donate to sustain healthy mangrove ecosystem. Also, PAHs and total nitrogen (TN) were crucial factors driving the soil bacterial community in Qi'ao sites, whereas in the Futian sites, PAHs and SOC were more important. PAHs, SOC and TN showed negative effects on specific bacteria abundance. Subsequently, environmental factors and PAHs levels influenced the soil bacterial ecological functions community. Co-occurrence network analysis revealed non-random assembly patterns of the bacterial communities. SBR1031 and A4b were the keystone genera and played a crucial role whgich played an irreplaceable role in PAHs degradation in Qi'ao and Futian sites. PAHs inhibited specific microbial activity and metabolism in native mangrove forest, while affects positively to bacterial community in riverine runoff outlet which might profoundly affect the whole soil quality under various vegetation types. Overall, this study might identify existing health problems and provide insights for enhancing protection and utilization management for mangrove ecosystem in the Greater Bay Area.
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Affiliation(s)
- Yining Wu
- Northeast Forestry University, China; Heilongjiang Academy of Sciences Institute of Natural Resources and Ecology, China
| | | | - Yu Zou
- Qiqihar Medical University, China
| | | | - He Wang
- Northeast Forestry University, China
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13
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Jia Y, Zhao S, Guo W, Peng L, Zhao F, Wang L, Fan G, Zhu Y, Xu D, Liu G, Wang R, Fang X, Zhang H, Kristiansen K, Zhang W, Chen J. Sequencing introduced false positive rare taxa lead to biased microbial community diversity, assembly, and interaction interpretation in amplicon studies. ENVIRONMENTAL MICROBIOME 2022; 17:43. [PMID: 35978448 PMCID: PMC9387074 DOI: 10.1186/s40793-022-00436-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 07/21/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Increasing studies have demonstrated potential disproportionate functional and ecological contributions of rare taxa in a microbial community. However, the study of the microbial rare biosphere is hampered by their inherent scarcity and the deficiency of currently available techniques. Sample-wise cross contaminations might be introduced by sample index misassignment in the most widely used metabarcoding amplicon sequencing approach. Although downstream bioinformatic quality control and clustering or denoising algorithms could remove sequencing errors and non-biological artifact reads, no algorithm could eliminate high quality reads from sample-wise cross contaminations introduced by index misassignment, making it difficult to distinguish between bona fide rare taxa and potential false positives in metabarcoding studies. RESULTS We thoroughly evaluated the rate of index misassignment of the widely used NovaSeq 6000 and DNBSEQ-G400 sequencing platforms using both commercial and customized mock communities, and observed significant lower (0.08% vs. 5.68%) fraction of potential false positive reads for DNBSEQ-G400 as compared to NovaSeq 6000. Significant batch effects could be caused by stochastically introduced false positive or false negative rare taxa. These false detections could also lead to inflated alpha diversity of relatively simple microbial communities and underestimated that of complex ones. Further test using a set of cow rumen samples reported differential rare taxa by different sequencing platforms. Correlation analysis of the rare taxa detected by each sequencing platform demonstrated that the rare taxa identified by DNBSEQ-G400 platform had a much higher possibility to be correlated with the physiochemical properties of rumen fluid as compared to NovaSeq 6000 platform. Community assembly mechanism and microbial network correlation analysis indicated that false positive or negative rare taxa detection could lead to biased community assembly mechanism and identification of fake keystone species of the community. CONCLUSIONS We highly suggest proper positive/negative/blank controls, technical replicate settings, and proper sequencing platform selection in future amplicon studies, especially when the microbial rare biosphere would be focused.
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Affiliation(s)
- Yangyang Jia
- BGI-Shenzhen, Shenzhen, 518083, China
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Shengguo Zhao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Wenjie Guo
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Ling Peng
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Fang Zhao
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Guangyi Fan
- BGI-Shenzhen, Shenzhen, 518083, China
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Yuanfang Zhu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Dayou Xu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Guilin Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Ruoqing Wang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | | | - He Zhang
- BGI-Shenzhen, Shenzhen, 518083, China
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Karsten Kristiansen
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Universitetsparken 13, 2100, Copenhagen, Denmark.
- Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, 266555, China.
| | - Wenwei Zhang
- BGI-Shenzhen, Shenzhen, 518083, China.
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China.
| | - Jianwei Chen
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China.
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Universitetsparken 13, 2100, Copenhagen, Denmark.
- Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, 266555, China.
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14
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Effects of Spartina alterniflora Invasion on Nitrogen Fixation and Phosphorus Solubilization in a Subtropical Marine Mangrove Ecosystem. Microbiol Spectr 2022; 10:e0068221. [PMID: 35604174 PMCID: PMC9241609 DOI: 10.1128/spectrum.00682-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This study revealed the efficient nutrient cycling mechanism of mangroves. Positive coupling effects were observed in sediment quality, NF and PS processes, and NFOPSMs with the invasion of
S. alterniflora
.
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15
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Yu T, Cheng L, Liu Q, Wang S, Zhou Y, Zhong H, Tang M, Nian H, Lian T. Effects of Waterlogging on Soybean Rhizosphere Bacterial Community Using V4, LoopSeq, and PacBio 16S rRNA Sequence. Microbiol Spectr 2022; 10:e0201121. [PMID: 35171049 PMCID: PMC8849089 DOI: 10.1128/spectrum.02011-21] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 01/16/2022] [Indexed: 12/26/2022] Open
Abstract
Waterlogging causes a significant reduction in soil oxygen levels, which in turn negatively affects soil nutrient use efficiency and crop yields. Rhizosphere microbes can help plants to better use nutrients and thus better adapt to this stress, while it is not clear how the plant-associated microbes respond to waterlogging stress. There are also few reports on whether this response is influenced by different sequencing methods and by different soils. In this study, using partial 16S rRNA sequencing targeting the V4 region and two full-length 16S rRNA sequencing approaches targeting the V1 to V9 regions, the effects of waterlogging on soybean rhizosphere bacterial structure in two types of soil were examined. Our results showed that, compared with the partial 16S sequencing, full-length sequencing, both LoopSeq and Pacific Bioscience (PacBio) 16S sequencing, had a higher resolution. On both types of soil, all the sequencing methods showed that waterlogging significantly affected the bacterial community structure of the soybean rhizosphere and increased the relative abundance of Geobacter. Furthermore, modular analysis of the cooccurrence network showed that waterlogging increased the relative abundance of some microorganisms related to nitrogen cycling when using V4 sequencing and increased the microorganisms related to phosphorus cycling when using LoopSeq and PacBio 16S sequencing methods. Core microorganism analysis further revealed that the enriched members of different species might play a central role in maintaining the stability of bacterial community structure and ecological functions. Together, our study explored the role of microorganisms enriched at the rhizosphere under waterlogging in assisting soybeans to resist stress. Furthermore, compared to partial and PacBio 16S sequencing, LoopSeq offers improved accuracy and reduced sequencing prices, respectively, and enables accurate species-level and strain identification from complex environmental microbiome samples. IMPORTANCE Soybeans are important oil-bearing crops, and waterlogging has caused substantial decreases in soybean production all over the world. The microbes associated with the host have shown the ability to promote plant growth, nutrient absorption, and abiotic resistance. High-throughput sequencing of partial 16S rRNA is the most commonly used method to analyze the microbial community. However, partial sequencing cannot provide correct classification information below the genus level, which greatly limits our research on microbial ecology. In this study, the effects of waterlogging on soybean rhizosphere microbial structure in two soil types were explored using partial 16S rRNA and full-length 16S gene sequencing by LoopSeq and Pacific Bioscience (PacBio). The results showed that full-length sequencing had higher classification resolution than partial sequencing. Three sequencing methods all indicated that rhizosphere bacterial community structure was significantly impacted by waterlogging, and the relative abundance of Geobacter was increased in the rhizosphere in both soil types after suffering waterlogging. Moreover, the core microorganisms obtained by different sequencing methods all contain species related to nitrogen cycling. Together, our study not only explored the role of microorganisms enriched at the rhizosphere level under waterlogging in assisting soybean to resist stress but also showed that LoopSeq sequencing is a less expensive and more convenient method for full-length sequencing by comparing different sequencing methods.
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Affiliation(s)
- Taobing Yu
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, People’s Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, People’s Republic of China
| | - Lang Cheng
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, People’s Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, People’s Republic of China
| | - Qi Liu
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, People’s Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, People’s Republic of China
| | - Shasha Wang
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, People’s Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, People’s Republic of China
| | - Yuan Zhou
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | | | | | - Hai Nian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, People’s Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, People’s Republic of China
| | - Tengxiang Lian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, People’s Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, People’s Republic of China
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Adi Wicaksono W, Reisenhofer-Graber T, Erschen S, Kusstatscher P, Berg C, Krause R, Cernava T, Berg G. Phyllosphere-associated microbiota in built environment: Do they have the potential to antagonize human pathogens? J Adv Res 2022; 43:109-121. [PMID: 36585101 PMCID: PMC9811327 DOI: 10.1016/j.jare.2022.02.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 02/01/2022] [Accepted: 02/09/2022] [Indexed: 02/06/2023] Open
Abstract
INTRODUCTION The plant microbiota is known to protect its host against invasion by plant pathogens. Recent studies have indicated that the microbiota of indoor plants is transmitted to the local built environment where it might fulfill yet unexplored functions. A better understanding of the interplay of such microbial communities with human pathogens might provide novel cues related to natural inhibition of them. OBJECTIVE We studied the plant microbiota of two model indoor plants, Musa acuminata and Chlorophytum comosum, and their effect on human pathogens. The main objective was to identify mechanisms by which the microbiota of indoor plants inhibits human-pathogenic bacteria. METHODS Microbial communities and functioning were investigated using a comprehensive set of experiments and methods combining amplicon and shotgun metagenomic analyses with results from interaction assays. RESULTS A diverse microbial community was found to be present on Musa and Chlorophytum grown in different indoor environments; the datasets comprised 1066 bacterial, 1261 fungal, and 358 archaeal ASVs. Bacterial communities were specific for each plant species, whereas fungal and archaeal communities were primarily shaped by the built environment. Sphingomonas and Bacillus were found to be prevalent components of a ubiquitous core microbiome in the two model plants; they are well-known for antagonistic activity towards plant pathogens. Interaction assays indicated that they can also antagonize opportunistic human pathogens. Moreover, the native plant microbiomes harbored a broad spectrum of biosynthetic gene clusters, and in parallel, a variety of antimicrobial resistance genes. By conducting comparative metagenomic analyses between plants and abiotic surfaces, we found that the phyllosphere microbiota harbors features that are clearly distinguishable from the surrounding abiotic surfaces. CONCLUSIONS Naturally occurring phyllosphere bacteria can potentially act as a protective shield against opportunistic human pathogens. This knowledge and the underlying mechanisms can provide an important basis to establish a healthy microbiome in built environments.
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Affiliation(s)
- Wisnu Adi Wicaksono
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria.
| | | | - Sabine Erschen
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria.
| | - Peter Kusstatscher
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria.
| | - Christian Berg
- Institute of Plant Sciences, Karl-Franzens-University, Graz, Austria.
| | - Robert Krause
- Department of Internal Medicine, Medical University of Graz, Graz, Austria; BioTechMed Graz, Inter-university Cooperation Platform, Graz, Austria.
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria; BioTechMed Graz, Inter-university Cooperation Platform, Graz, Austria.
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria; BioTechMed Graz, Inter-university Cooperation Platform, Graz, Austria; Leibniz Institute for Agricultural Engineering and Bioeconomy Potsdam, Potsdam, Germany; Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany.
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Puthusseri RM, Nair HP, Johny TK, Bhat SG. Insights into the response of mangrove sediment microbiomes to heavy metal pollution: Ecological risk assessment and metagenomics perspectives. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 298:113492. [PMID: 34385112 DOI: 10.1016/j.jenvman.2021.113492] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 08/03/2021] [Accepted: 08/05/2021] [Indexed: 06/13/2023]
Abstract
Rapid urbanisation and ensuing anthropogenic pollution lead to an escalated occurrence of heavy metals and metal-resistant bacteria in the soil ecosystem. Mangrove ecosystems are particularly vulnerable to heavy metal bioaccumulation and often act as metal sinks of the coastal areas. As a consequence, the microbial population in mangrove sediments develop multifarious metal tolerance mechanisms to combat metal toxicity. In this context, metagenomic investigation of two mangroves, viz. Mangalavanam and Puthuvypin from the heavily populated metropolitan city, Cochin (Central Kerala, India) was undertaken to discern the metal resistance functions and taxonomic diversity of the microbial consortia. Estimation of heavy metal content using Inductively Coupled Plasma Atomic Emission Spectrometer (ICP-MS) identified the abundance of zinc, chromium, nickel copper, lead, arsenic, and cadmium in the mangrove sediments. Ecological risk index values indicated high cadmium contamination of the two estuarine samples. Whole metagenome shotgun sequencing of the Central Kerala mangroves and comparative analysis with mangrove metal resistomes from other geographical regions revealed the prevalence of cobalt-zinc-cadmium resistance and preponderance of Proteobacteria in all the datasets. Cation efflux system protein CusA constituted the majority of the reads at the function level. Comparative analysis of taxonomy identified the dominance of Anaeromyxobacter, Geobacter, Pseudomonas, Candidatus Solibacter, and Pelobacter in the mangrove datasets. Non-metric multidimensional scaling analysis of the metal resistance genes depicted strong geographical clustering of the function and composition of metal resistant bacteria, suggesting a strong innate resilience of microbiome towards anthropogenic perturbations. More robust studies with intensive sampling will enhance our understanding of the occurrence, interactions, and functions of microbial heavy metal resistome in mangrove ecosystems.
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Affiliation(s)
- Rinu Madhu Puthusseri
- Department of Biotechnology, Cochin University of Science and Technology, Cochin, 682022, India.
| | - Harisree Paramel Nair
- School of Life Science, Faculty of Science and Engineering, Anglia Ruskin University, East Road, Cambridge Campus, East Rd, Cambridge, CB1 1PT, UK.
| | - Tina Kollannoor Johny
- Department of Biotechnology, Cochin University of Science and Technology, Cochin, 682022, India.
| | - Sarita Ganapathy Bhat
- Department of Biotechnology, Cochin University of Science and Technology, Cochin, 682022, India.
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Luo Z, Zhong Q, Han X, Hu R, Liu X, Xu W, Wu Y, Huang W, Zhou Z, Zhuang W, Yan Q, He Z, Wang C. Depth-dependent variability of biological nitrogen fixation and diazotrophic communities in mangrove sediments. MICROBIOME 2021; 9:212. [PMID: 34702367 PMCID: PMC8549172 DOI: 10.1186/s40168-021-01164-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 09/17/2021] [Indexed: 05/29/2023]
Abstract
BACKGROUND Nitrogen-fixing prokaryotes (diazotrophs) contribute substantially to nitrogen input in mangrove sediments, and their structure and nitrogen fixation rate (NFR) are significantly controlled by environmental conditions. Despite the well-known studies on diazotrophs in surficial sediments, the diversity, structure, and ecological functions of diazotrophic communities along environmental gradients of mangrove sediment across different depths are largely unknown. Here, we investigated how biological nitrogen fixation varied with the depth of mangrove sediments from the perspectives of both NFR and diazotrophic communities. RESULTS Through acetylene reduction assay, nifH gene amplicon and metagenomic sequencing, we found that the NFR increased but the diversity of diazotrophic communities decreased with the depth of mangrove sediments. The structure of diazotrophic communities at different depths was largely driven by salinity and exhibited a clear divergence at the partitioning depth of 50 cm. Among diazotrophic genera correlated with NFR, Agrobacterium and Azotobacter were specifically enriched at 50-100 cm sediments, while Anaeromyxobacter, Rubrivivax, Methylocystis, Dickeya, and Methylomonas were more abundant at 0-50 cm. Consistent with the higher NFR, metagenomic analysis demonstrated the elevated abundance of nitrogen fixation genes (nifH/D/K) in deep sediments, where nitrification genes (amoA/B/C) and denitrification genes (nirK and norB) became less abundant. Three metagenome-assembled genomes (MAGs) of diazotrophs from deep mangrove sediments indicated their facultatively anaerobic and mixotrophic lifestyles as they contained genes for low-oxygen-dependent metabolism, hydrogenotrophic respiration, carbon fixation, and pyruvate fermentation. CONCLUSIONS This study demonstrates the depth-dependent variability of biological nitrogen fixation in terms of NFR and diazotrophic communities, which to a certain extent relieves the degree of nitrogen limitation in deep mangrove sediments. Video Abstract.
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Affiliation(s)
- Zhiwen Luo
- 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
| | - Qiuping Zhong
- 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
| | - Xingguo Han
- Institute of Biogeochemistry and Pollutant Dynamics, Swiss Federal Institute of Technology, Zurich (ETH Zurich), Universitätstrasse 16, 8092, Zurich, Switzerland
| | - Ruiwen Hu
- 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
| | - Xingyu Liu
- 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
| | - Wenjun Xu
- South China Institute of Environmental Sciences, Ministry of Ecology and Environment, Guangzhou, 510530, PR China
| | - Yongjie Wu
- South China Institute of Environmental Sciences, Ministry of Ecology and Environment, Guangzhou, 510530, PR China
| | - Weiming Huang
- 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
| | - Zhengyuan Zhou
- 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
| | - Wei Zhuang
- 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
| | - 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
| | - 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
| | - Cheng 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.
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Shah RM, Hillyer KE, Stephenson S, Crosswell J, Karpe AV, Palombo EA, Jones OAH, Gorman D, Bodrossy L, van de Kamp J, Bissett A, Whiteley AS, Steven ADL, Beale DJ. Functional analysis of pristine estuarine marine sediments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 781:146526. [PMID: 33798899 DOI: 10.1016/j.scitotenv.2021.146526] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/10/2021] [Accepted: 03/12/2021] [Indexed: 06/12/2023]
Abstract
Traditional environmental monitoring techniques are well suited to resolving acute exposure effects but lack resolution in determining subtle shifts in ecosystem functions resulting from chronic exposure(s). Surveillance with sensitive omics-based technologies could bridge this gap but, to date, most omics-based environmental studies have focused on previously degraded environments, identifying key metabolic differences resulting from anthropogenic perturbations. Here, we apply omics-based approaches to pristine environments to establish blueprints of microbial functionality within healthy estuarine sediment communities. We collected surface sediments (n = 50) from four pristine estuaries along the Western Cape York Peninsula of Far North Queensland, Australia. Sediment microbiomes were analyzed for 16S rRNA amplicon sequences, central carbon metabolism metabolites and associated secondary metabolites via targeted and untargeted metabolic profiling methods. Multivariate statistical analyses indicated heterogeneity among all the sampled estuaries, however, taxa-function relationships could be established that predicted community metabolism potential. Twenty-four correlated gene-metabolite pathways were identified and used to establish sediment microbial blueprints of essential carbon metabolism and amino acid biosynthesis that were positively correlated with community metabolic function outputs (2-oxisocapraote, tryptophan, histidine citrulline and succinic acid). In addition, an increase in the 125 KEGG genes related to metal homeostasis and metal resistance was observed, although, none of the detected metabolites related to these specific genes upon integration. However, there was a correlation between metal abundance and functional genes related to Fe and Zn metabolism. Our results establish a baseline microbial blueprint for the pristine sediment microbiome, one that drives important ecosystem services and to which future ecosurveillance monitoring can be compared.
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Affiliation(s)
- Rohan M Shah
- Land and Water, Commonwealth Scientific and Industrial Research Organisation, Dutton Park, QLD 4102, Australia; Department of Chemistry and Biotechnology, School of Science, Swinburne University of Technology, Hawthorn, VIC 3122, Australia
| | - Katie E Hillyer
- Land and Water, Commonwealth Scientific and Industrial Research Organisation, Dutton Park, QLD 4102, Australia
| | - Sarah Stephenson
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Lucas Heights, NSW 2234, Australia
| | - Joseph Crosswell
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Dutton Park, QLD 4102, Australia
| | - Avinash V Karpe
- Land and Water, Commonwealth Scientific and Industrial Research Organisation, Dutton Park, QLD 4102, Australia
| | - Enzo A Palombo
- Department of Chemistry and Biotechnology, School of Science, Swinburne University of Technology, Hawthorn, VIC 3122, Australia
| | - Oliver A H Jones
- Australian Centre for Research on Separation Science (ACROSS), School of Science, RMIT University, Bundoora West Campus, PO Box 71, Bundoora, VIC 3083, Australia
| | - Daniel Gorman
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Indian Ocean Marine Research Centre, Crawley, WA 6009, Australia
| | - Levente Bodrossy
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Battery Point, TAS 7004, Australia
| | - Jodie van de Kamp
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Battery Point, TAS 7004, Australia
| | - Andrew Bissett
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Battery Point, TAS 7004, Australia
| | - Andrew S Whiteley
- Land and Water, Commonwealth Scientific and Industrial Research Organisation, Floreat, WA 6014, Australia
| | - Andy D L Steven
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Dutton Park, QLD 4102, Australia
| | - David J Beale
- Land and Water, Commonwealth Scientific and Industrial Research Organisation, Dutton Park, QLD 4102, Australia.
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20
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Navarrete-Euan H, Rodríguez-Escamilla Z, Pérez-Rueda E, Escalante-Herrera K, Martínez-Núñez MA. Comparing Sediment Microbiomes in Contaminated and Pristine Wetlands along the Coast of Yucatan. Microorganisms 2021; 9:877. [PMID: 33923859 PMCID: PMC8073884 DOI: 10.3390/microorganisms9040877] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/02/2021] [Accepted: 04/03/2021] [Indexed: 12/27/2022] Open
Abstract
Microbial communities are important players in coastal sediments for the functioning of the ecosystem and the regulation of biogeochemical cycles. They also have great potential as indicators of environmental perturbations. To assess how microbial communities can change their composition and abundance along coastal areas, we analyzed the composition of the microbiome of four locations of the Yucatan Peninsula using 16S rRNA gene amplicon sequencing. To this end, sediment from two conserved (El Palmar and Bocas de Dzilam) and two contaminated locations (Sisal and Progreso) from the coast northwest of the Yucatan Peninsula in three different years, 2017, 2018 and 2019, were sampled and sequenced. Microbial communities were found to be significantly different between the locations. The most noticeable difference was the greater relative abundance of Planctomycetes present at the conserved locations, versus FBP group found with greater abundance in contaminated locations. In addition to the difference in taxonomic groups composition, there is a variation in evenness, which results in the samples of Bocas de Dzilam and Progreso being grouped separately from those obtained in El Palmar and Sisal. We also carry out the functional prediction of the metabolic capacities of the microbial communities analyzed, identifying differences in their functional profiles. Our results indicate that landscape of the coastal microbiome of Yucatan sediment shows changes along the coastline, reflecting the constant dynamics of coastal environments and their impact on microbial diversity.
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Affiliation(s)
- Herón Navarrete-Euan
- UMDI-Sisal, Facultad de Ciencias, Universidad Nacional Autónoma de México, Parque Científico y Tecnológico de Yucatán, Sierra Papacal-Chuburna Km 5, Mérida, Yucatán 97302, Mexico; (H.N.-E.); (Z.R.-E.); (K.E.-H.)
| | - Zuemy Rodríguez-Escamilla
- UMDI-Sisal, Facultad de Ciencias, Universidad Nacional Autónoma de México, Parque Científico y Tecnológico de Yucatán, Sierra Papacal-Chuburna Km 5, Mérida, Yucatán 97302, Mexico; (H.N.-E.); (Z.R.-E.); (K.E.-H.)
| | - Ernesto Pérez-Rueda
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, UNAM, Unidad Académica Yucatán, Mérida, Yucatán 97302, Mexico;
| | - Karla Escalante-Herrera
- UMDI-Sisal, Facultad de Ciencias, Universidad Nacional Autónoma de México, Parque Científico y Tecnológico de Yucatán, Sierra Papacal-Chuburna Km 5, Mérida, Yucatán 97302, Mexico; (H.N.-E.); (Z.R.-E.); (K.E.-H.)
| | - Mario Alberto Martínez-Núñez
- UMDI-Sisal, Facultad de Ciencias, Universidad Nacional Autónoma de México, Parque Científico y Tecnológico de Yucatán, Sierra Papacal-Chuburna Km 5, Mérida, Yucatán 97302, Mexico; (H.N.-E.); (Z.R.-E.); (K.E.-H.)
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