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Wani AK, Qadir F, Elboughdiri N, Rahayu F, Saefudin, Pranowo D, Martasari C, Kosmiatin M, Suhara C, Sudaryono T, Prayogo Y, Yadav KK, Muzammil K, Eltayeb LB, Alreshidi MA, Singh R. Metagenomics and plant-microbe symbioses: Microbial community dynamics, functional roles in carbon sequestration, nitrogen transformation, sulfur and phosphorus mobilization for sustainable soil health. Biotechnol Adv 2025; 82:108580. [PMID: 40246210 DOI: 10.1016/j.biotechadv.2025.108580] [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: 01/16/2025] [Revised: 03/19/2025] [Accepted: 04/13/2025] [Indexed: 04/19/2025]
Abstract
Biogeochemical cycles are fundamental processes that regulate the flow of essential elements such as carbon, nitrogen, and phosphorus, sustaining ecosystem productivity and global biogeochemical equilibrium. These cycles are intricately influenced by plant-microbe symbioses, which facilitate nutrient acquisition, organic matter decomposition, and the transformation of soil nutrients. Through mutualistic interactions, plants and microbes co-regulate nutrient availability and promote ecosystem resilience, especially under environmental stress. Metagenomics has emerged as a transformative tool for deciphering the complex microbial communities and functional genes driving these cycles. By enabling the high-throughput sequencing and annotation of microbial genomes, metagenomics provides unparalleled insights into the taxonomic diversity, metabolic potential, and functional pathways underlying microbial contributions to biogeochemical processes. Unlike previous reviews, this work integrates recent advancements in metagenomics with complementary omics approaches to provide a comprehensive perspective on how plant-microbe interactions modulate biogeochemical cycles at molecular, genetic, and ecosystem levels. By highlighting novel microbial processes and potential biotechnological applications, this review aims to guide future research in leveraging plant-microbe symbioses for sustainable agriculture, ecosystem restoration, and climate change mitigation.
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Affiliation(s)
- Atif Khurshid Wani
- School of Bioengineering and Biosciences, Lovely Professional University, Jalandhar 144411, Punjab, India.
| | - Fayzan Qadir
- Department of Civil Engineering, Engineering & Technology, Jamia Millia Islamia-Jamia Nagar, New Delhi 110025, India
| | - Noureddine Elboughdiri
- Chemical Engineering Department, College of Engineering, University of Ha'il, P.O. Box 2440, Ha'il 81441, Saudi Arabia
| | - Farida Rahayu
- Research Center for Genetic Engineering, National Research and Innovation Agency, Bogor 16911, Indonesia
| | - Saefudin
- Research Center for Estate Crop, National Research and Innovation Agency, Bogor 16111, Indonesia
| | - Dibyo Pranowo
- Research Center for Estate Crop, National Research and Innovation Agency, Bogor 16111, Indonesia
| | - Chaireni Martasari
- Research Center for Horticulture, National Research and Innovation Agency, Bogor 16111, Indonesia
| | - Mia Kosmiatin
- Research Center for Horticulture, National Research and Innovation Agency, Bogor 16111, Indonesia
| | - Cece Suhara
- Research Center for Estate Crop, National Research and Innovation Agency, Bogor 16111, Indonesia
| | - Tri Sudaryono
- Research Center for Horticulture, National Research and Innovation Agency, Bogor 16111, Indonesia
| | - Yusmani Prayogo
- Food Crops Research Center, National Research and Innovation Agency, Bogor 16111, Indonesia
| | - Krishna Kumar Yadav
- Department of VLSI Microelectronics, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai -602105, Tamil Nadu, India; Environmental and Atmospheric Sciences Research Group, Scientific Research Center, Al-Ayen University, Nasiriyah, Thi-Qar, Iraq
| | - Khursheed Muzammil
- Department of Public Health, College of Applied Medical Sciences, Khamis Mushait, King Khalid University, Abha 62561, Saudi Arabia
| | - Lienda Bashier Eltayeb
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam Bin AbdulAziz University- Al-Kharj, 11942 Riyadh, Saudi Arabia
| | - Maha Awjan Alreshidi
- Department of Chemistry, College of Science, University of Ha'il, Ha'il 81441, Saudi Arabia
| | - Reena Singh
- School of Bioengineering and Biosciences, Lovely Professional University, Jalandhar 144411, Punjab, India
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Liu Y, Chen S, Liang J, Song J, Sun Y, Liao R, Liang M, Cao H, Chen X, Wu Y, Bei L, Pan Y, Yan B, Li Y, Tao Y, Bu R, Gong B. Bacterial Community Structure and Environmental Driving Factors in the Surface Sediments of Six Mangrove Sites from Guangxi, China. Microorganisms 2024; 12:2607. [PMID: 39770809 PMCID: PMC11678403 DOI: 10.3390/microorganisms12122607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2024] [Revised: 11/27/2024] [Accepted: 12/13/2024] [Indexed: 01/11/2025] Open
Abstract
Mangroves, as blue carbon reservoirs, provide a unique habitat for supporting a variety of microorganisms. Among these, bacteria play crucial roles in the biogeochemical processes of mangrove sediments. However, little is known about their community composition, spatial distribution patterns, and environmental driving factors, particularly across the large geographical scales of mangrove wetlands. In this study, the composition and spatial distribution of the bacterial community structure and its response to fifteen physicochemical parameters (including temperature, pH, salinity, moisture, clay, silt, sand, organic carbon (OC), total nitrogen (TN), total phosphorus (TP), inorganic phosphorus (IP), organic phosphorus (OP), δ13C, δ15N, and carbon/nitrogen ratio (C/N ratio)) were characterized in 32 sampling locations of six different mangrove habitats from Guangxi, China, applying 16S rRNA gene high-throughput sequencing technology and correlation analysis. Our results indicated that the spatial distribution patterns in bacterial communities were significantly different among the six different mangrove sites, as evidenced by NMDS (non-metric multidimensional scaling), ANOSIM (analysis of similarity), and LDA (linear discriminant analysis) analysis. Composition analysis of bacterial communities showed that overall, Chloroflexi (8.3-31.6%), Proteobacteria (13.6-30.1%), Bacteroidota (5.0-24.6%), and Desulfobacterota (3.8-24.0%) were the most abundant bacterial phyla in the mangrove surface sediments. Redundancy analysis (RDA) further highlighted that salinity, δ13C, temperature, δ15N, and silt were the most critical environmental variables influencing the composition of bacterial communities across the whole mangrove samples. Notably, Chloroflexi, one of the most abundant bacterial phyla in the mangrove wetlands, displayed a significantly positive correlation with OC and a negative correlation with δ13C, suggesting its essential role in the degradation of terrestrial-derived organic carbon. These findings support the current understanding of the roles of the bacterial communities and their interactions with environmental factors in diverse mangrove ecosystems.
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Affiliation(s)
- Ying Liu
- Pinglu Canal and Beibu Gulf Coastal Ecosystem Observation and Research Station of Guangxi, Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou 535011, China; (Y.L.); (J.L.); (J.S.); (Y.S.); (R.L.); (M.L.); (H.C.); (X.C.); (Y.W.); (L.B.); (Y.P.); (B.Y.); (Y.L.); (Y.T.)
| | - Songze Chen
- Shenzhen Ecological and Environmental Monitoring Center of Guangdong Province, Shenzhen 518049, China;
| | - Jinyu Liang
- Pinglu Canal and Beibu Gulf Coastal Ecosystem Observation and Research Station of Guangxi, Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou 535011, China; (Y.L.); (J.L.); (J.S.); (Y.S.); (R.L.); (M.L.); (H.C.); (X.C.); (Y.W.); (L.B.); (Y.P.); (B.Y.); (Y.L.); (Y.T.)
| | - Jingjing Song
- Pinglu Canal and Beibu Gulf Coastal Ecosystem Observation and Research Station of Guangxi, Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou 535011, China; (Y.L.); (J.L.); (J.S.); (Y.S.); (R.L.); (M.L.); (H.C.); (X.C.); (Y.W.); (L.B.); (Y.P.); (B.Y.); (Y.L.); (Y.T.)
| | - Yue Sun
- Pinglu Canal and Beibu Gulf Coastal Ecosystem Observation and Research Station of Guangxi, Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou 535011, China; (Y.L.); (J.L.); (J.S.); (Y.S.); (R.L.); (M.L.); (H.C.); (X.C.); (Y.W.); (L.B.); (Y.P.); (B.Y.); (Y.L.); (Y.T.)
| | - Riquan Liao
- Pinglu Canal and Beibu Gulf Coastal Ecosystem Observation and Research Station of Guangxi, Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou 535011, China; (Y.L.); (J.L.); (J.S.); (Y.S.); (R.L.); (M.L.); (H.C.); (X.C.); (Y.W.); (L.B.); (Y.P.); (B.Y.); (Y.L.); (Y.T.)
| | - Mingzhong Liang
- Pinglu Canal and Beibu Gulf Coastal Ecosystem Observation and Research Station of Guangxi, Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou 535011, China; (Y.L.); (J.L.); (J.S.); (Y.S.); (R.L.); (M.L.); (H.C.); (X.C.); (Y.W.); (L.B.); (Y.P.); (B.Y.); (Y.L.); (Y.T.)
| | - Hongming Cao
- Pinglu Canal and Beibu Gulf Coastal Ecosystem Observation and Research Station of Guangxi, Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou 535011, China; (Y.L.); (J.L.); (J.S.); (Y.S.); (R.L.); (M.L.); (H.C.); (X.C.); (Y.W.); (L.B.); (Y.P.); (B.Y.); (Y.L.); (Y.T.)
| | - Xiuhao Chen
- Pinglu Canal and Beibu Gulf Coastal Ecosystem Observation and Research Station of Guangxi, Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou 535011, China; (Y.L.); (J.L.); (J.S.); (Y.S.); (R.L.); (M.L.); (H.C.); (X.C.); (Y.W.); (L.B.); (Y.P.); (B.Y.); (Y.L.); (Y.T.)
| | - Yuxia Wu
- Pinglu Canal and Beibu Gulf Coastal Ecosystem Observation and Research Station of Guangxi, Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou 535011, China; (Y.L.); (J.L.); (J.S.); (Y.S.); (R.L.); (M.L.); (H.C.); (X.C.); (Y.W.); (L.B.); (Y.P.); (B.Y.); (Y.L.); (Y.T.)
| | - Liting Bei
- Pinglu Canal and Beibu Gulf Coastal Ecosystem Observation and Research Station of Guangxi, Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou 535011, China; (Y.L.); (J.L.); (J.S.); (Y.S.); (R.L.); (M.L.); (H.C.); (X.C.); (Y.W.); (L.B.); (Y.P.); (B.Y.); (Y.L.); (Y.T.)
| | - Yuting Pan
- Pinglu Canal and Beibu Gulf Coastal Ecosystem Observation and Research Station of Guangxi, Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou 535011, China; (Y.L.); (J.L.); (J.S.); (Y.S.); (R.L.); (M.L.); (H.C.); (X.C.); (Y.W.); (L.B.); (Y.P.); (B.Y.); (Y.L.); (Y.T.)
| | - Baishu Yan
- Pinglu Canal and Beibu Gulf Coastal Ecosystem Observation and Research Station of Guangxi, Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou 535011, China; (Y.L.); (J.L.); (J.S.); (Y.S.); (R.L.); (M.L.); (H.C.); (X.C.); (Y.W.); (L.B.); (Y.P.); (B.Y.); (Y.L.); (Y.T.)
| | - Yunru Li
- Pinglu Canal and Beibu Gulf Coastal Ecosystem Observation and Research Station of Guangxi, Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou 535011, China; (Y.L.); (J.L.); (J.S.); (Y.S.); (R.L.); (M.L.); (H.C.); (X.C.); (Y.W.); (L.B.); (Y.P.); (B.Y.); (Y.L.); (Y.T.)
| | - Yun Tao
- Pinglu Canal and Beibu Gulf Coastal Ecosystem Observation and Research Station of Guangxi, Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou 535011, China; (Y.L.); (J.L.); (J.S.); (Y.S.); (R.L.); (M.L.); (H.C.); (X.C.); (Y.W.); (L.B.); (Y.P.); (B.Y.); (Y.L.); (Y.T.)
| | - Rongping Bu
- Pinglu Canal and Beibu Gulf Coastal Ecosystem Observation and Research Station of Guangxi, Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou 535011, China; (Y.L.); (J.L.); (J.S.); (Y.S.); (R.L.); (M.L.); (H.C.); (X.C.); (Y.W.); (L.B.); (Y.P.); (B.Y.); (Y.L.); (Y.T.)
| | - Bin Gong
- Pinglu Canal and Beibu Gulf Coastal Ecosystem Observation and Research Station of Guangxi, Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou 535011, China; (Y.L.); (J.L.); (J.S.); (Y.S.); (R.L.); (M.L.); (H.C.); (X.C.); (Y.W.); (L.B.); (Y.P.); (B.Y.); (Y.L.); (Y.T.)
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Cai Q, Obieze CC, Pyke R, Delorme K, Maynard C, Greer CW, Khasa D. Gradient of acid mine drainage regulates microbial community assembly and the diversity of species associated with native plants. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 363:125059. [PMID: 39362621 DOI: 10.1016/j.envpol.2024.125059] [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: 06/11/2024] [Revised: 09/13/2024] [Accepted: 09/30/2024] [Indexed: 10/05/2024]
Abstract
Acid mine drainage (AMD) is considered as one of the most important global environmental challenges. Therefore, understanding the impact of AMD on the diversity of microbial communities associated with native plants is important for phytoremediation. In this study, the community assembly and microbial diversity associated with native plants growing along an AMD impact gradient was investigated using metabarcoding and high throughput iChip technique. The study revealed that across both domains of bacteria and fungi, richness and species diversity decreased according to AMD impact. Bacterial species diversity was more stratified according to the pH gradient than fungi, and the AMD impact on the plant-associated microbial diversity decreased towards the plant roots. The microbial community composition of the undisturbed site was significantly different from the AMD impacted sites, and the communities in the AMD impacted sites were further stratified according to the degree of impact. The overall microbial diversity was mediated by the AMD impact, niche differences and plant species differences. Dispersal limitation was the most important community assembly process in the undisturbed site, while the homogenous selection of Burkholderia, Actinospica, Puia and Bradyrhizobium increased along the AMD impact gradient. Differential abundance analysis further revealed that Umbelopsis, Burkholderia and Sphingomonas were among the biomarkers of the AMD impacted sites. Several strains of some of these responsive genera were subsequently isolated using the iChip. Overall, this study presents novel insight into the ecology of plant-associated microbial communities that are relevant for environmental monitoring and for enhancing the revegetation of AMD impacted sites.
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Affiliation(s)
- Qinhong Cai
- Department of Natural Resource Sciences, McGill University, Canada.
| | - Chinedu C Obieze
- Institut de biologie intégrative et des systèmes, Université Laval, Canada.
| | - Ruby Pyke
- Department of Natural Resource Sciences, McGill University, Canada
| | - Karine Delorme
- Department of Natural Resource Sciences, McGill University, Canada
| | - Christine Maynard
- Energy, Mining and Environment Research Centre, National Research Council Canada, Canada
| | - Charles W Greer
- Department of Natural Resource Sciences, McGill University, Canada; Energy, Mining and Environment Research Centre, National Research Council Canada, Canada
| | - Damase Khasa
- Institut de biologie intégrative et des systèmes, Université Laval, Canada
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Um S, Jeong H, Park JE, Seo J, Jung SH, Bae M, Lee KT, Moon K. Isolation and Characterization of Bioactive Compounds from Saccharomonospora sp. CMS18 and Their Antifungal Properties. Mar Drugs 2024; 22:539. [PMID: 39728114 DOI: 10.3390/md22120539] [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: 10/26/2024] [Revised: 11/26/2024] [Accepted: 11/28/2024] [Indexed: 12/28/2024] Open
Abstract
In this study, metagenomic analysis was employed to investigate the bacterial communities in the Muan tidal mudflat of the Republic of Korea. We used metagenomic analysis to identify the microbial community in tidal soil dominated by Proteobacteria. From this environment, the bacterial strain, Saccharomonospora sp. CMS18, was isolated and yielded two previously unknown compounds, penipaline D (3) and N-acetyl-dimethylallyltryptophan (4). The chemical structures of the isolated compounds along with 6-dimethylallyl-indole (1), 6-dimethylallyltryptophan (2), penipaline D (3), and N-acetyl-dimethylallyltryptophan (4) were structurally investigated using HR-ESI-MS and NMR spectroscopy. The isolated compound 6-dimethylallyl-indole (1) demonstrated broad-spectrum antifungal activity, with IC50 value of 0.04 mM against Candida glabrata and 0.35 mM against both Candida albicans and Cryptococcus neoformans. Additionally, it exhibited additive interaction with caspofungin against C. albicans.
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Affiliation(s)
- Soohyun Um
- College of Pharmacy, Yonsei University, Incheon 21983, Republic of Korea
| | - Hyeongju Jeong
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Ji-Eun Park
- Korea Research Institute for Veterinary Biologics, Iksan 54531, Republic of Korea
- Korea Zoonosis Research Institute, Jeonbuk National University, Iksan 54531, Republic of Korea
| | - Jeongwon Seo
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Sang Heon Jung
- College of Pharmacy, Gachon University, Incheon 21936, Republic of Korea
| | - Munhyung Bae
- College of Pharmacy, Gachon University, Incheon 21936, Republic of Korea
| | - Kyung-Tae Lee
- Korea Zoonosis Research Institute, Jeonbuk National University, Iksan 54531, Republic of Korea
| | - Kyuho Moon
- College of Pharmacy, Kyung Hee University, Seoul 02447, Republic of Korea
- Department of Biomedical and Pharmaceutical Sciences, Graduate School, Kyung Hee University, Seoul 02447, Republic of Korea
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Fiard M, Militon C, Sylvi L, Migeot J, Michaud E, Jézéquel R, Gilbert F, Bihannic I, Devesa J, Dirberg G, Cuny P. Uncovering potential mangrove microbial bioindicators to assess urban and agricultural pressures on Martinique island in the eastern Caribbean Sea. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 928:172217. [PMID: 38583633 DOI: 10.1016/j.scitotenv.2024.172217] [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: 01/12/2024] [Revised: 04/02/2024] [Accepted: 04/02/2024] [Indexed: 04/09/2024]
Abstract
Martinique's mangroves, which cover 1.85 ha of the island (<0.1 % of the total area), are considerably vulnerable to local urban, agricultural, and industrial pollutants. Unlike for temperate ecosystems, there are limited indicators that can be used to assess the anthropogenic pressures on mangroves. This study investigated four stations on Martinique Island, with each being subject to varying anthropogenic pressures. An analysis of mangrove sediment cores approximately 18 cm in depth revealed two primary types of pressures on Martinique mangroves: (i) an enrichment in organic matter in the two stations within the highly urbanized bay of Fort-de-France and (ii) agricultural pressure observed in the four studied mangrove stations. This pressure was characterized by contamination, exceeding the regulatory thresholds, with dieldrin, total DDT, and metals (As, Cu and Ni) found in phytosanitary products. The mangroves of Martinique are subjected to varying degrees of anthropogenic pressure, but all are subjected to contamination by organochlorine pesticides. Mangroves within the bay of Fort-de-France experience notably higher pressures compared to those in the island's northern and southern regions. In these contexts, the microbial communities exhibited distinct responses. The microbial biomass and the abundance of bacteria and archaea were higher in the two less-impacted stations, while in the mangrove of Fort-de-France, various phyla typically associated with polluted environments were more prevalent. These differences in the microbiota composition led to the identification of 65 taxa, including Acanthopleuribacteraceae, Spirochaetaceae, and Pirellulaceae, that could potentially serve as indicators of an anthropogenic influence on the mangrove sediments of Martinique Island.
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Affiliation(s)
- Maud Fiard
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
| | - Cécile Militon
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
| | - Léa Sylvi
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
| | - Jonathan Migeot
- Impact Mer consulting, expertise, and R&D firm, 20 rue Karukéra, 97200 Fort de France, Martinique/FWI, France.
| | - Emma Michaud
- Univ Brest, CNRS, IRD, Ifremer, LEMAR, 29280 Plouzané, France.
| | - Ronan Jézéquel
- CEDRE, 715 rue Alain Colas, 29218 Brest CEDEX 2, France.
| | - Franck Gilbert
- Laboratoire Écologie Fonctionnelle et Environnement, Université de Toulouse, CNRS, Toulouse INP, Université Toulouse 3 - Paul Sabatier, Toulouse, France.
| | | | - Jeremy Devesa
- Univ Brest, CNRS, IRD, Ifremer, LEMAR, 29280 Plouzané, France.
| | - Guillaume Dirberg
- Biologie des Organismes et Ecosystèmes Aquatiques (UMR 8067 BOREA) Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, IRD, UCN, UA, Rue Buffon, 75005 Paris, France.
| | - Philippe Cuny
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
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Nakashima Y, Sonobe T, Hanada M, Kitano G, Sonoyama Y, Iwai K, Kimura T, Kusube M. Microbial Detoxification of Sediments Underpins Persistence of Zostera marina Meadows. Int J Mol Sci 2024; 25:5442. [PMID: 38791480 PMCID: PMC11122150 DOI: 10.3390/ijms25105442] [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: 03/29/2024] [Revised: 05/13/2024] [Accepted: 05/14/2024] [Indexed: 05/26/2024] Open
Abstract
Eelgrass meadows have attracted much attention not only for their ability to maintain marine ecosystems as feeding grounds for marine organisms but also for their potential to store atmospheric and dissolved CO2 as blue carbon. This study comprehensively evaluated the bacterial and chemical data obtained from eelgrass sediments of different scales along the Japanese coast to investigate the effect on the acclimatization of eelgrass. Regardless of the eelgrass habitat, approximately 1% Anaerolineales, Babeliales, Cytophagales, and Phycisphaerales was present in the bottom sediment. Sulfate-reducing bacteria (SRB) were present at 3.69% in eelgrass sediment compared to 1.70% in bare sediment. Sulfur-oxidizing bacteria (SOB) were present at 2.81% and 1.10% in the eelgrass and bare sediment, respectively. Bacterial composition analysis and linear discriminant analysis revealed that SOB detoxified H2S in the eelgrass meadows and that the larger-scale eelgrass meadows had a higher diversity of SOB. Our result indicated that there were regional differences in the system that detoxifies H2S in eelgrass meadows, either microbial oxidation mediated by SOB or O2 permeation via the physical diffusion of benthos. However, since bacterial flora and phylogenetic analyses cannot show bias and/or causality due to PCR, future kinetic studies on microbial metabolism are expected.
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Affiliation(s)
- Yuki Nakashima
- Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Osaka, Japan;
- Advanced Engineering Faculty, National Institute of Technology, Wakayama College, Gobo 644-0023, Wakayama, Japan
| | - Takumi Sonobe
- Advanced Engineering Faculty, National Institute of Technology, Wakayama College, Gobo 644-0023, Wakayama, Japan
| | - Masashi Hanada
- Promotion of Technical Support, National Institute of Technology, Wakayama College, Gobo 644-0023, Wakayama, Japan
| | - Goushi Kitano
- Agri-Light Lab. Inc., Minamata 867-0068, Kumamoto, Japan
| | | | - Katsumi Iwai
- Study Team for Creation of Waterfront, Yokohama 220-0023, Kanagawa, Japan
| | - Takashi Kimura
- Study Team for Creation of Waterfront, Yokohama 220-0023, Kanagawa, Japan
| | - Masataka Kusube
- Department of Applied Chemistry and Biochemistry, National Institute of Technology, Wakayama College, Gobo 644-0023, Wakayama, Japan
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Jia W, Huang P, Zhu K, Gao X, Chen Q, Chen J, Ran Y, Chen S, Ma M, Wu S. Zonation of bulk and rhizosphere soil bacterial communities and their covariation patterns along the elevation gradient in riparian zones of three Gorges reservoir, China. ENVIRONMENTAL RESEARCH 2024; 249:118383. [PMID: 38331152 DOI: 10.1016/j.envres.2024.118383] [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: 11/23/2023] [Revised: 01/26/2024] [Accepted: 01/30/2024] [Indexed: 02/10/2024]
Abstract
Zonation is a typical pattern of soil distribution and species assembly across riparian habitats. Microorganisms are essential members of riparian ecosystems and whether soil microbial communities demonstrate similar zonation patterns and how bulk and rhizosphere soil microorganisms interact along the elevation (submergence stress) gradient remain largely unknown. In this study, bulk and rhizosphere (dominant plant) soil samples were collected and investigated across riparian zones where the submergence stress intensity increased as the elevation decreased. Results showed that the richness of bacterial communities in bulk and rhizosphere soil samples was significantly different and presented a zonation pattern along with the submergence stress gradient. Bulk soil at medium elevation that underwent moderate submergence stress had the most abundant bacterial communities, while the species richness of rhizobacteria at low elevation that experienced serious submergence stress was the highest. Additionally, principal coordinate analysis (PCoA) and significance tests showed that bulk and rhizosphere soil samples were distinguished according to the structure of bacterial communities, and so were bulk or rhizosphere soil samples from different elevations. Redundancy analysis (RDA) and Mantel test suggested that bacterial communities of bulk soil mainly relied on the contents of soil organic matter, total carbon (TC), total nitrogen (TN), sodium (Na), calcium (Ca) and magnesium (Mg). Contrastingly, the contents of Na and Mg were the main factors explaining the variation in rhizobacterial community composition. Correlation and microbial source tracking analyses showed thatthe relationship of bulk and rhizosphere soil bacteria became much stronger, and the rhizosphere soil may get more bacterial communities from bulk soil with the increase in submergence severity. Our results suggest that the abiotic and biotic components of the riparian ecosystem are closely covariant along the submergence stress gradient and imply that the bacterial community may be a key node linking soil physiochemical properties and vegetation communities.
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Affiliation(s)
- Weitao Jia
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
| | - Ping Huang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
| | - Kai Zhu
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
| | - Xin Gao
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
| | - Qiao Chen
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
| | - Jilong Chen
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
| | - Yiguo Ran
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
| | - Shanshan Chen
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
| | - Maohua Ma
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
| | - Shengjun Wu
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China.
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8
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Muwawa EM, Makonde HM, Obieze CC, de Oliveira IG, Jefwa JM, Kahindi JHP, Khasa DP. Diversity and assembly patterns of mangrove rhizosphere mycobiome along the Coast of Gazi Bay and Mida Creek in Kenya. PLoS One 2024; 19:e0298237. [PMID: 38635689 PMCID: PMC11025898 DOI: 10.1371/journal.pone.0298237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 01/19/2024] [Indexed: 04/20/2024] Open
Abstract
Fungi are among key actors in the biogeochemical processes occurring in mangrove ecosystems. In this study, we investigated the changes of fungal communities in selected mangrove species by exploring differences in diversity, structure and the degree of ecological rearrangement occurring within the rhizospheres of four mangrove species (Sonneratia alba, Rhizophora mucronata, Ceriops tagal and Avicennia marina) at Gazi Bay and Mida Creek in Kenya. Alpha diversity investigation revealed that there were no significant differences in species diversity between the same mangrove species in the different sites. Rather, significant differences were observed in fungal richness for some of the mangrove species. Chemical parameters of the mangrove sediment significantly correlated with fungal alpha diversity and inversely with richness. The fungal community structure was significantly differentiated by mangrove species, geographical location and chemical parameters. Taxonomic analysis revealed that 96% of the amplicon sequence variants belonged to the Phylum Ascomycota, followed by Basidiomycota (3%). Predictive FUNGuild and co-occurrence network analysis revealed that the fungal communities in Gazi Bay were metabolically more diverse compared to those of Mida Creek. Overall, our results demonstrate that anthropogenic activities influenced fungal richness, community assembly and their potential ecological functions in the mangrove ecosystems investigated.
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Affiliation(s)
- Edith M. Muwawa
- Department of Biological Sciences, Pwani University, Kilifi, Kenya
- Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, Canada
| | - Huxley M. Makonde
- Department of Pure & Applied Sciences, Technical University of Mombasa, Mombasa, Kenya
| | - Chinedu C. Obieze
- Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, Canada
| | - Isabelle G. de Oliveira
- Laboratory of Mycorrhizal Associations, Department of Microbiology/BIOAGRO, Universidade Federal de Vicosa, Vicosa-MG, Brazil
| | - Joyce M. Jefwa
- Department of Biological Sciences, Pwani University, Kilifi, Kenya
| | | | - Damase P. Khasa
- Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, Canada
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Mlewski EC, Saona LA, Boidi FJ, Chiappero MF, Vaieretti MV, Soria M, Farías ME, Izquierdo AE. Exploring Soil Bacterial Diversity in Relation to Edaphic Physicochemical Properties of High-altitude Wetlands from Argentine Puna. MICROBIAL ECOLOGY 2023; 87:6. [PMID: 38030916 DOI: 10.1007/s00248-023-02316-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 11/13/2023] [Indexed: 12/01/2023]
Abstract
High Andean wetlands, particularly those known as vegas or bofedales, are essential conservation ecosystems due to their significant contribution to ecosystem services. The soil microbial communities in these ecosystems play a crucial role in fundamental processes such as decomposition and nutrient cycling, sustaining life in the region. However, at present, these microbial communities are poorly understood. In order to contribute to this knowledge, we aimed to characterize and compare the microbial communities from soils of seven Argentine Puna vegas and to analyze their association with soil physicochemical characteristics. Proteobacteria (Gamma and Alphaproteobacteria) was the dominant phylum across all vegas, followed in abundance by Actinobacteriota, Desulfobacterota, and Chloroflexi. Furthermore, the abundance of specific bacterial families and genera varied significantly between the vegas; some of them can be associated with plant growth-promoting bacteria such as Rhodomicrobium in La Quebradita and Quebrada del Diablo, Bacillus in Antofalla and Las Quinuas. Laguna Negra showed no shared ASVs with abundance in genera such as Sphingomonas and Pseudonocardia. The studied vegas also differed in their soil physicochemical properties; however, associations between the composition of microbial communities with the edaphic parameters measured were not found. These results suggest that other environmental factors (e.g., geographic, climatic, and plant communities' characteristics) could determine soil microbial diversity patterns. Further investigations are needed to be focused on understanding the composition and function of microorganisms in the soil associated with specific vegetation types in these high-altitude wetlands, which will provide valuable insights into the ecological dynamics of these ecosystems for conservation strategies.
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Affiliation(s)
- Estela Cecilia Mlewski
- Instituto Multidisciplinario de Biología Vegetal (IMBiV), CONICET-Universidad Nacional de Córdoba, Córdoba, Argentina
- Facultad de Ciencias Exactas Físicas y Naturales, Centro de Ecología y Recursos Naturales Renovables (CERNAR), Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Luis A Saona
- Facultad de Química y Biología, Departamento de Biología, Universidad de Santiago de Chile, Santiago, Chile
- Millennium Nucleus of Patagonian Limit of Life (LiLi), Valdivia, Chile
| | - Flavia Jaquelina Boidi
- Instituto Nacional de Tecnología Agropecuaria (INTA), EEA Rafaela, Rafaela, Argentina
- Instituto de Investigación de la Cadena Láctea (IDICAL, CONICET-INTA), Rafaela, Argentina
| | - M Fernanda Chiappero
- Instituto Multidisciplinario de Biología Vegetal (IMBiV), CONICET-Universidad Nacional de Córdoba, Córdoba, Argentina
| | - María Victoria Vaieretti
- Instituto Multidisciplinario de Biología Vegetal (IMBiV), CONICET-Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Mariana Soria
- PUNABIO S.A. Campus USP-T Av. Solano Vera y Camino a Villa Nougués San Pablo, Tucumán, Argentina
| | - María Eugenia Farías
- PUNABIO S.A. Campus USP-T Av. Solano Vera y Camino a Villa Nougués San Pablo, Tucumán, Argentina
| | - Andrea E Izquierdo
- Instituto Multidisciplinario de Biología Vegetal (IMBiV), CONICET-Universidad Nacional de Córdoba, Córdoba, Argentina.
- Facultad de Ciencias Naturales y Exactas e Instituto M. Lillo, Universidad Nacional de Tucumán, San Miguel de Tucumán, Argentina.
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10
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Sui J, He X, Yi G, Zhou L, Liu S, Chen Q, Xiao X, Wu J. Diversity and structure of the root-associated bacterial microbiomes of four mangrove tree species, revealed by high-throughput sequencing. PeerJ 2023; 11:e16156. [PMID: 37810771 PMCID: PMC10559887 DOI: 10.7717/peerj.16156] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 08/31/2023] [Indexed: 10/10/2023] Open
Abstract
Background Root-associated microbes of the mangrove trees play important roles in protecting and maintaining mangrove ecosystems. At present, most of our understanding of mangrove root-related microbial diversity is obtained from specific mangrove species in selected geographic regions. Relatively little is known about the composition of the bacterial microbiota existing in disparate mangrove species microenvironments, particularly the relationship among different mangrove species in tropical environments. Methods We collected the root, rhizosphere soil, and non-rhizosphere soil of four mangrove trees (Acanthus ilicifolius, Bruguiera gymnorrhiza, Clerodendrum inerme, and Lumnitzera racemosa) and detected the 16S rRNA gene by a conventional PCR. We performed high throughput sequencing using Illumina Novaseq 6000 platform (2 × 250 paired ends) to investigate the bacterial communities related with the different mangrove species. Results We analyzed the bacterial diversity and composition related to the diverse ecological niches of mangrove species. Our data confirmed distinct distribution patterns of bacterial communities in the three rhizocompartments of the four mangrove species. Microbiome composition varied with compartments and host mangrove species. The bacterial communities between the endosphere and the other two compartments were distinctly diverse independent of mangrove species. The large degree of overlap in critical community members of the same rhizocompartment across distinct mangrove species was found at the phylum level. Furthermore, this is the first report of Acidothermus found in mangrove environments. In conclusion, understanding the complicated host-microbe associations in different mangrove species could lay the foundation for the exploitation of the microbial resource and the production of secondary metabolites.
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Affiliation(s)
- Jinlei Sui
- Public Research Center, Hainan Medical College, Haikou, China
| | - Xiaowen He
- Public Research Center, Hainan Medical College, Haikou, China
| | - Guohui Yi
- Public Research Center, Hainan Medical College, Haikou, China
| | - Limin Zhou
- Public Research Center, Hainan Medical College, Haikou, China
| | - Shunqing Liu
- Public Research Center, Hainan Medical College, Haikou, China
| | - Qianqian Chen
- Public Research Center, Hainan Medical College, Haikou, China
| | - Xiaohu Xiao
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Jinyan Wu
- Public Research Center, Hainan Medical College, Haikou, China
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11
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Bindajam AA, Mallick J, Talukdar S, Shohan AAA, Alshayeb MJ. Assessment of long-term mangrove distribution using optimised machine learning algorithms and landscape pattern analysis. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023:10.1007/s11356-023-27395-2. [PMID: 37195618 DOI: 10.1007/s11356-023-27395-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Accepted: 04/28/2023] [Indexed: 05/18/2023]
Abstract
Mangrove ecosystems provide numerous benefits, including carbon storage, coastal protection and food for marine organisms. However, mapping and monitoring of mangrove status in some regions, such as the Red Sea area, has been hindered by a lack of data, accurate and precise maps and technical expertise. In this study, an advanced machine learning algorithm was proposed to produce an accurate and precise high-resolution land use map that includes mangroves in the Al Wajh Bank habitat in northeastern Saudi Arabia. To achieve this, high-resolution multispectral images were generated using an image fusion technique, and machine learning algorithms were applied, including artificial neural networks, random forests and support vector machine algorithms. The performance of the models was evaluated using various matrices, and changes in mangrove distribution and connectivity were assessed using the landscape fragmentation model and Getis-Ord statistics. The research gap that this study aims to address is the lack of accurate and precise mapping and assessment of mangrove status in the Red Sea area, particularly in data-scarce regions. Our study produced high-resolution mobile laser scanning (MLS) imagery of 15-m length for 2014 and 2022, and trained 5, 6 and 9 models for artificial neural networks, support vector machines and random forests (RF) to predict land use and land cover maps using 15-m and 30-m resolution MLS images. The best models were identified using error matrices, and it was found that RF outperformed other models. According to the 15-m resolution map of 2022 and the best models of RF, the mangrove cover in the Al Wajh Bank is 27.6 km2, which increased to 34.99 km2 in the case of the 30-m resolution image of 2022, and was 11.94 km2 in 2014, indicating a doubling of the mangrove area. Landscape structure analysis revealed an increase in small core and hotspot areas, which were converted into medium core and very large hotspot areas in 2014. New mangrove areas were identified in the form of patches, edges, potholes and coldspots. The connectivity model showed an increase in connectivity over time, promoting biodiversity. Our study contributes to the promotion of the protection, conservation and planting of mangroves in the Red Sea area.
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Affiliation(s)
- Ahmed Ali Bindajam
- Department of Architecture and Planning, College of Engineering, King Khalid University, Abha, Kingdom of Saudi Arabia
| | - Javed Mallick
- Department of Civil Engineering, College of Engineering, King Khalid University, P.O. Box 394, Abha, 61411, Kingdom of Saudi Arabia.
| | - Swapan Talukdar
- Department of Geography, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi, India
| | - Ahmed Ali A Shohan
- Department of Architecture and Planning, College of Engineering, King Khalid University, Abha, Kingdom of Saudi Arabia
| | - Mohammed J Alshayeb
- Department of Architecture and Planning, College of Engineering, King Khalid University, Abha, Kingdom of Saudi Arabia
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12
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Liu L, Wang N, Liu M, Guo Z, Shi S. Assembly processes underlying bacterial community differentiation among geographically close mangrove forests. MLIFE 2023; 2:73-88. [PMID: 38818341 PMCID: PMC10989747 DOI: 10.1002/mlf2.12060] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 02/01/2023] [Accepted: 02/14/2023] [Indexed: 06/01/2024]
Abstract
Bacterial communities play pivotal roles in nutrient cycling in mangrove forests. The assembly of mangrove microbial communities has been found to be influenced by complex factors, such as geographic distance, physicochemical conditions, and plant identity, but the relative importance of these factors and how these factors shape the assembling process remain elusive. We analyzed the bacterial communities sampled from three mangrove species (Aegiceras corniculatum, Bruguiera sexangula, and Kandelia obovata) at three locations along the estuarine Dongzhai Harbor in Hainan, China. We revealed larger differences in rhizosphere bacterial communities among geographical locations than among plant species, indicated by differences in diversity, composition, and interaction networks. We found that dispersal limitation and homogeneous selection have substantial contributions to the assembly of mangrove rhizosphere bacterial communities in all three locations. Following the phylogenetic-bin-based null model analysis (iCAMP) framework, we also found dispersal limitation and homogeneous selection showing dominance in some bins. The greater differences among geographic locations may be mainly attributed to the larger proportions of dispersal limitation even at such a short geographic distance. We also found that beta diversity was positively correlated with environmental distances, implying that the more similar environmental conditions (such as rich carbon and nitrogen contents) among plant species may have shaped similar bacterial communities. We concluded that the geographic distances, which are associated with dispersal limitation, played a key role in assembling mangrove rhizosphere bacterial communities, while physicochemical conditions and plant identity contributed less.
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Affiliation(s)
- Lu Liu
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
| | - Nan Wang
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
| | - Min Liu
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
| | - Zixiao Guo
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
| | - Suhua Shi
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
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Song L, Wang Q, Wang P, Wu J. Benthic bacterial communities and bacteria–environment interactions after Kandelia obovata introduction and Spartina alterniflora invasion in Yueqing Bay, China. REGIONAL STUDIES IN MARINE SCIENCE 2023; 58:102787. [DOI: 10.1016/j.rsma.2022.102787] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2024]
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Conte C, Apostolaki ET, Vizzini S, Migliore L. A Tight Interaction between the Native Seagrass Cymodocea nodosa and the Exotic Halophila stipulacea in the Aegean Sea Highlights Seagrass Holobiont Variations. PLANTS (BASEL, SWITZERLAND) 2023; 12:350. [PMID: 36679063 PMCID: PMC9863530 DOI: 10.3390/plants12020350] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/03/2023] [Accepted: 01/05/2023] [Indexed: 06/17/2023]
Abstract
Seagrasses harbour bacterial communities with which they constitute a functional unit called holobiont that responds as a whole to environmental changes. Epiphytic bacterial communities rapidly respond to both biotic and abiotic factors, potentially contributing to the host fitness. The Lessepsian migrant Halophila stipulacea has a high phenotypical plasticity and harbours a highly diverse epiphytic bacterial community, which could support its invasiveness in the Mediterranean Sea. The current study aimed to evaluate the Halophila/Cymodocea competition in the Aegean Sea by analysing each of the two seagrasses in a meadow zone where these intermingled, as well as in their monospecific zones, at two depths. Differences in holobionts were evaluated using seagrass descriptors (morphometric, biochemical, elemental, and isotopic composition) to assess host changes, and 16S rRNA gene to identify bacterial community structure and composition. An Indicator Species Index was used to identify bacteria significantly associated with each host. In mixed meadows, native C. nodosa was shown to be affected by the presence of exotic H. stipulacea, in terms of both plant descriptors and bacterial communities, while H. stipulacea responded only to environmental factors rather than C. nodosa proximity. This study provided evidence of the competitive advantage of H. stipulacea on C. nodosa in the Aegean Sea and suggests the possible use of associated bacterial communities as an ecological seagrass descriptor.
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Affiliation(s)
- Chiara Conte
- PhD Program in Evolutionary Biology and Ecology, University of Rome Tor Vergata, 00133 Rome, Italy
- Laboratory of Ecology and Ecotoxicology, Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Eugenia T. Apostolaki
- Institute of Oceanography, Hellenic Centre for Marine Research, P.O. Box 2214, 71003 Heraklion, Crete, Greece
| | - Salvatrice Vizzini
- Department of Earth and Marine Sciences, University of Palermo, Via Archirafi 18, 90123 Palermo, Italy
- CoNISMa, National Interuniversity Consortium for Marine Sciences, Piazzale Flaminio 9, 00196 Roma, Italy
| | - Luciana Migliore
- Laboratory of Ecology and Ecotoxicology, Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy
- eCampus University, Via Isimbardi 10, 22060 Novedrate (CO), Italy
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15
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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: 1.7] [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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Navgire GS, Goel N, Sawhney G, Sharma M, Kaushik P, Mohanta YK, Mohanta TK, Al-Harrasi A. Analysis and Interpretation of metagenomics data: an approach. Biol Proced Online 2022; 24:18. [PMID: 36402995 PMCID: PMC9675974 DOI: 10.1186/s12575-022-00179-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 10/19/2022] [Indexed: 11/20/2022] Open
Abstract
Advances in next-generation sequencing technologies have accelerated the momentum of metagenomic studies, which is increasing yearly. The metagenomics field is one of the versatile applications in microbiology, where any interaction in the environment involving microorganisms can be the topic of study. Due to this versatility, the number of applications of this omics technology reached its horizons. Agriculture is a crucial sector involving crop plants and microorganisms interacting together. Hence, studying these interactions through the lenses of metagenomics would completely disclose a new meaning to crop health and development. The rhizosphere is an essential reservoir of the microbial community for agricultural soil. Hence, we focus on the R&D of metagenomic studies on the rhizosphere of crops such as rice, wheat, legumes, chickpea, and sorghum. These recent developments are impossible without the continuous advancement seen in the next-generation sequencing platforms; thus, a brief introduction and analysis of the available sequencing platforms are presented here to have a clear picture of the workflow. Concluding the topic is the discussion about different pipelines applied to analyze data produced by sequencing techniques and have a significant role in interpreting the outcome of a particular experiment. A plethora of different software and tools are incorporated in the automated pipelines or individually available to perform manual metagenomic analysis. Here we describe 8-10 advanced, efficient pipelines used for analysis that explain their respective workflows to simplify the whole analysis process.
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Affiliation(s)
- Gauri S Navgire
- Department of Microbiology, Savitribai Phule Pune University, Pune, Maharastra, 411007, India
| | - Neha Goel
- Department of Genetics and Tree Improvement, Forest Research Institute, 248006, Dehradun, India
| | - Gifty Sawhney
- Inflammation Pharmacology Division, Academy of Scientific and Innovative Research (AcSIR), CSIR-Indian Institute of Integrative Medicine, Jammu-180001, Jammu Kashmir, India
| | - Mohit Sharma
- Department of Molecular Medicine, Medical University of Warsaw and Malopolska Center of Biotechnology, Karkow, Poland
| | | | | | - Tapan Kumar Mohanta
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, 616, Oman.
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, 616, Oman.
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Kenya E, Kinyanjui G, Kipnyargis A, Kinyua F, Mwangi M, Khamis F, Mwirichia R. Amplicon-based assessment of bacterial diversity and community structure in three tropical forest soils in Kenya. Heliyon 2022; 8:e11577. [PMID: 36411924 PMCID: PMC9674510 DOI: 10.1016/j.heliyon.2022.e11577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 07/14/2022] [Accepted: 11/07/2022] [Indexed: 11/16/2022] Open
Abstract
Forest soils provide a multitude of habitats for diverse communities of bacteria. In this study, we selected three tropical forests in Kenya to determine the diversity and community structure of soil bacteria inhabiting these regions. Kakamega and Irangi are rainforests, whereas Gazi Bay harbors mangrove forests. The three natural forests occupy different altitudinal zones and differ in their environmental characteristics. Soil samples were collected from a total of 12 sites and soil physicochemical parameters for each sampling site were analyzed. We used an amplicon-based Illumina high-throughput sequencing approach. Total community DNA was extracted from individual samples using the phenol-chloroform method. The 16S ribosomal RNA gene segment spanning the V4 region was amplified using the Illumina MiSeq platform. Diversity indices, rarefaction curves, hierarchical clustering, principal component analysis (PCA), and non-metric multidimensional scaling (NMDS) analyses were performed in R software. A total of 13,410 OTUs were observed at 97% sequence similarity. Bacterial communities were dominated by Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria, and Acidobacteria in both rainforest and mangrove sampling sites. Alpha diversity indices and species richness were higher in Kakamega and Irangi rainforests compared to mangroves in Gazi Bay. The composition of bacterial communities within and between the three forests was also significantly differentiated (R = 0.559, p = 0.007). Clustering in both PCA and NMDS plots showed that each sampling site had a distinct bacterial community profile. The NMDS analysis also indicated that soil EC, sodium, sulfur, magnesium, boron, and manganese contributed significantly to the observed variation in the bacterial community structure. Overall, this study demonstrated the presence of diverse taxa and heterogeneous community structures of soil bacteria inhabiting three tropical forests of Kenya. Our results also indicated that variation in soil chemical parameters was the major driver of the observed bacterial diversity and community structure in these forests.
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Affiliation(s)
- Eucharia Kenya
- Department of Biological Sciences, University of Embu, P. O. Box 6-60100, Embu, Kenya
| | - Grace Kinyanjui
- Department of Biological Sciences, University of Embu, P. O. Box 6-60100, Embu, Kenya
| | - Alex Kipnyargis
- Department of Biological Sciences, University of Embu, P. O. Box 6-60100, Embu, Kenya
| | - Franklin Kinyua
- Department of Biological Sciences, University of Embu, P. O. Box 6-60100, Embu, Kenya
| | - Mary Mwangi
- Department of Biochemistry and Biotechnology, Kenyatta University, P. O. Box 43844-00100, Nairobi, Kenya
| | - Fathiya Khamis
- International Centre of Insect Physiology and Ecology (ICIPE), P. O. Box 30772-00100, Nairobi, Kenya
| | - Romano Mwirichia
- Department of Biological Sciences, University of Embu, P. O. Box 6-60100, Embu, Kenya
- Corresponding author.
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18
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Obieze CC, Wani GA, Shah MA, Reshi ZA, Comeau AM, Khasa DP. Anthropogenic activities and geographic locations regulate microbial diversity, community assembly and species sorting in Canadian and Indian freshwater lakes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 826:154292. [PMID: 35248630 DOI: 10.1016/j.scitotenv.2022.154292] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 02/13/2022] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
Freshwater lakes are important reservoirs and sources of drinking water globally. However, the microbiota, which supports the functionality of these ecosystems is threatened by the influx of nutrients, heavy metals and other toxic chemical substances from anthropogenic activities. The influence of these factors on the diversity, assembly mechanisms and co-occurrence patterns of bacterial communities in freshwater lakes is not clearly understood. Hence, samples were collected from six different impacted lakes in Canada and India and examined by 454-pyrosequencing technology. The trophic status of these lakes was determined using specific chemical parameters. Our results revealed that bacterial diversity and community composition was altered by both the lake water chemistry and geographic distance. Anthropogenic activities pervasively influenced species distribution. Dispersal limitation (32.3%), homogenous selection (31.8%) and drift (20%) accounted for the largest proportions of the bacterial community assembly mechanisms. Homogenous selection increased in lakes with higher nutrient concentration, while stochasticity reduced. Community functional profiles revealed that deterministic processes dominated the assembly mechanisms of phylotypes with higher potential for biodegradation, while stochasticity dominated the assembly of phylotypes with potential for antimicrobial resistance. Bacteroidota (44%) and Proteobacteria (34%) were the most abundant phyla. Co-occurrence network analysis revealed that complexity increased in more impacted lakes, while competition and the nature of anthropogenic activity contributed to species sorting. Overall, this study demonstrates that bacterial community changes in freshwater lakes are linked to anthropogenic activities, with corresponding consequences on the distribution of phylotypes of environmental and human health interest.
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Affiliation(s)
- Chinedu C Obieze
- Centre for Forest Research, Institute of Integrative Biology and Systems, Université Laval, Quebec, QC G1V0A6, Canada.
| | - Gowher A Wani
- Centre for Forest Research, Institute of Integrative Biology and Systems, Université Laval, Quebec, QC G1V0A6, Canada; Department of Botany, University of Kashmir, Srinagar 190006, Jammu and Kashmir, India
| | - Manzoor A Shah
- Department of Botany, University of Kashmir, Srinagar 190006, Jammu and Kashmir, India
| | - Zafar A Reshi
- Department of Botany, University of Kashmir, Srinagar 190006, Jammu and Kashmir, India
| | - André M Comeau
- Integrated Microbiome Resource, Dalhousie University, Halifax, NS, Canada
| | - Damase P Khasa
- Centre for Forest Research, Institute of Integrative Biology and Systems and Canada Research Chair in Forest Genomics, Université Laval, Quebec, QC G1V0A6, Canada
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19
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Li L, Peng C, Yang Z, He Y, Liang M, Cao H, Qiu Q, Song J, Su Y, Gong B. Microbial communities in swamps of four mangrove reserves driven by interactions between physicochemical properties and microbe in the North Beibu Gulf, China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:37582-37597. [PMID: 35066825 DOI: 10.1007/s11356-021-18134-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 12/11/2021] [Indexed: 06/14/2023]
Abstract
Mangroves are distributed in coastal and estuarine regions and are characterized as a sink for terrestrial pollution. It is believed that complex interactions between environmental factors and microbial communities exist in mangrove swamps. However, little is known about environment-microbe interactions. There is a need to clarify some important environmental factors shaping microbial communities and how environmental factors interact with microbial assemblages in mangrove swamps. In the present study, physicochemical and microbial characteristics in four mangrove reserves (named ZZW, Qin, Bei, and GQ) in the North Beibu Gulf were determined. The interactions between environmental factors and microbial assemblages were analyzed with statistical methods in addition to CCA and RDA. Higher concentrations of sulfate (SO42--S) and Fe but lower concentrations of total phosphorus (TP) and NO3--N were detected in ZZW and Qin. Nutrient elements (NO3--N, NH4+-N, organic matter (OM), SO42--S, Fe, and TP) were more important than heavy metals for determining the microbial assemblages, and NO3--N was the most important factor. NO3--N, SO42--S, TP, and Fe formed a significant co-occurrence network in conjunction with some bacterial taxa, most of which were Proteobacteria. Notably, comparatively elevated amounts of sulfate-reducing bacteria (Desulfatibacillum, Desulfomonile, and Desulfatiglans) and sulfur-oxidizing bacteria (Thioprofundum and Thiohalophilus) were found in ZZW and Qin. The co-occurrence network suggested that some bacteria involved in sulfate reduction and sulfur oxidation drive the transformation of P and N, resulting in the reduction of P and N in mangrove swamps. Through the additional utilization of multivariate regression tree (MRT) and co-occurrence network analysis, our research provides a new perspective for understanding the interactions between environmental factors and microbial communities in mangroves.
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Affiliation(s)
- Lu Li
- The Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou, 535011, China
| | - Chunyan Peng
- The Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou, 535011, China
| | - Zicong Yang
- The Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou, 535011, China
| | - Yu He
- The Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou, 535011, China
| | - Meng Liang
- The Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou, 535011, China
| | - Hongmin Cao
- The Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou, 535011, China
| | - Qinghua Qiu
- The Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou, 535011, China
| | - Jingjing Song
- The Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou, 535011, China.
| | - Youlu Su
- Innovative Institute of Animal Healthy Breeding, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China.
| | - Bin Gong
- The Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou, 535011, China.
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Wu S, Wang J, Wang J, Du X, Ran Q, Chen Q, Sheng D, Li YZ. Halalkalibacterium roseum gen. nov., sp. nov., a new member of the family Balneolaceae isolated from soil. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005339] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, non-motile, moderately halophilic and facultatively anaerobic bacterium, designated YR4-1T, was isolated from a saline-alkali and sorghum-planting soil sample collected in Dongying, Shandong Province, PR China. Growth occurred at 28–45 °C with the presence of 4.0–20.0 % (w/v) NaCl and pH 6.0–9.0. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that YR4-1T shared the highest similarity of 92.1–92.4 % with the valid published species of
Aliifodinibius
. The isolate formed a separate clade at the genus level in recently described family
Balneolaceae
. The draft genome of strain YR4-1T is 3.83 Mbp long with 44.0 mol% G+C content. The strain possesses several genes involved in the osmotic stress response mechanism and diverse metabolic pathways, probably for the living in saline environment. This may lead to a better understanding of the underrepresented
Balneolaceae
lineage. The major menaquinone was MK-7. The main polar lipid profile was composed of diphosphatidylglycerol, phosphatidylglycerol, phosphoglycolipids, aminophosphoglycolipid, one glycolipid, and four unidentified lipids. The predominant cellular fatty acids were iso-C15 : 0 (35.7 %) and anteiso-C15 : 0 (33.5 %). On the basis of its phenotypic, chemotaxonomic and phylogenetic features, strain YR4-1T represents a novel species of a new genus, for which the name Halalkalibacterium roseum gen. nov., sp. nov. is proposed. The type strain is YR4-1T (=CGMCC 1.17777T=KCTC 72795T).
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Affiliation(s)
- Shuge Wu
- State Key Laboratory of Microbial Technology, Institute of Microbiology Technology, Shandong University, Qingdao 266237, PR China
| | - Jingjing Wang
- State Key Laboratory of Microbial Technology, Institute of Microbiology Technology, Shandong University, Qingdao 266237, PR China
| | - Jianing Wang
- State Key Laboratory of Microbial Technology, Institute of Microbiology Technology, Shandong University, Qingdao 266237, PR China
| | - Xinran Du
- State Key Laboratory of Microbial Technology, Institute of Microbiology Technology, Shandong University, Qingdao 266237, PR China
| | - Qi Ran
- State Key Laboratory of Microbial Technology, Institute of Microbiology Technology, Shandong University, Qingdao 266237, PR China
| | - Qi Chen
- State Key Laboratory of Microbial Technology, Institute of Microbiology Technology, Shandong University, Qingdao 266237, PR China
| | - Duohong Sheng
- State Key Laboratory of Microbial Technology, Institute of Microbiology Technology, Shandong University, Qingdao 266237, PR China
| | - Yue-zhong Li
- State Key Laboratory of Microbial Technology, Institute of Microbiology Technology, Shandong University, Qingdao 266237, PR China
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21
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Li Y, Wang Y, Shen C, Xu L, Yi S, Zhao Y, Zuo W, Gu C, Shan Y, Bai Y. Structural and Predicted Functional Diversities of Bacterial Microbiome in Response to Sewage Sludge Amendment in Coastal Mudflat Soil. BIOLOGY 2021; 10:biology10121302. [PMID: 34943217 PMCID: PMC8698727 DOI: 10.3390/biology10121302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/04/2021] [Accepted: 12/06/2021] [Indexed: 11/16/2022]
Abstract
The study investigated the influence of sewage sludge application at rates of 0 (CK), 30 (ST), 75 (MT), and 150 (HT) t ha−1 to mudflats on bacterial community diversity and predicted functions using amplicon-based sequencing. Soils under sewage sludge treatments, especially the HT treatment, exhibited lower pH, salinity and higher nutrient contents (C, N, and P). Moreover, restructured bacterial communities with significantly higher diversities and distinct core and unique microbiomes were observed in all sewage sludge-amended soils as compared to the control. Specifically, core bacterial families, such as Hyphomicrobiaceae, Cytophagaceae, Pirellulaceae Microbacteriaceae, and Phyllobacteriaceae, were significantly enriched in sewage sludge-amended soils. In addition, sewage sludge amendment significantly improved predicted functional diversities of core microbiomes, with significantly higher accumulative relative abundances of functions related to carbon and nitrogen cycling processes compared to the unamended treatment. Correlation analyses showed that modified soil physicochemical properties were conducive for the improvement of diversities of bacterial communities and predicted functionalities. These outcomes demonstrated that sewage sludge amendment not only alleviated saline–sodic and nutrient deficiency conditions, but also restructured bacterial communities with higher diversities and versatile functions, which may be particularly important for the fertility formation and development of mudflat soils.
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Affiliation(s)
- Yunlong Li
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou 225127, China; (Y.L.); (Y.W.); (C.S.); (L.X.); (S.Y.); (Y.Z.); (W.Z.); (Y.S.)
| | - Yimin Wang
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou 225127, China; (Y.L.); (Y.W.); (C.S.); (L.X.); (S.Y.); (Y.Z.); (W.Z.); (Y.S.)
| | - Chao Shen
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou 225127, China; (Y.L.); (Y.W.); (C.S.); (L.X.); (S.Y.); (Y.Z.); (W.Z.); (Y.S.)
| | - Lu Xu
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou 225127, China; (Y.L.); (Y.W.); (C.S.); (L.X.); (S.Y.); (Y.Z.); (W.Z.); (Y.S.)
| | - Siqiang Yi
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou 225127, China; (Y.L.); (Y.W.); (C.S.); (L.X.); (S.Y.); (Y.Z.); (W.Z.); (Y.S.)
| | - Yilin Zhao
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou 225127, China; (Y.L.); (Y.W.); (C.S.); (L.X.); (S.Y.); (Y.Z.); (W.Z.); (Y.S.)
| | - Wengang Zuo
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou 225127, China; (Y.L.); (Y.W.); (C.S.); (L.X.); (S.Y.); (Y.Z.); (W.Z.); (Y.S.)
| | - Chuanhui Gu
- Environmental Research Center, Duke Kunshan University, Kunshan 215316, China;
| | - Yuhua Shan
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou 225127, China; (Y.L.); (Y.W.); (C.S.); (L.X.); (S.Y.); (Y.Z.); (W.Z.); (Y.S.)
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing 210095, China
| | - Yanchao Bai
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou 225127, China; (Y.L.); (Y.W.); (C.S.); (L.X.); (S.Y.); (Y.Z.); (W.Z.); (Y.S.)
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing 210095, China
- Correspondence:
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22
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Ruen-Pham K, Graham LE, Satjarak A. Spatial Variation of Cladophora Epiphytes in the Nan River, Thailand. PLANTS (BASEL, SWITZERLAND) 2021; 10:2266. [PMID: 34834629 PMCID: PMC8622721 DOI: 10.3390/plants10112266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/19/2021] [Accepted: 10/20/2021] [Indexed: 11/16/2022]
Abstract
Cladophora is an algal genus known to be ecologically important. It provides habitats for microorganisms known to provide ecological services such as biosynthesis of cobalamin (vitamin B12) and nutrient cycling. Most knowledge of microbiomes was obtained from studies of lacustrine Cladophora species. However, whether lotic freshwater Cladophora microbiomes are as complex as the lentic ones or provide similar ecological services is not known. To illuminate these issues, we used amplicons of 16S rDNA, 18S rDNA, and ITS to investigate the taxonomy and diversity of the microorganisms associated with replicate Cladophora samples from three sites along the Nan River, Thailand. Results showed that the diversity of prokaryotic and eukaryotic members of Cladophora microbiomes collected from different sampling sites was statistically different. Fifty percent of the identifiable taxa were shared across sampling sites: these included organisms belonging to different trophic levels, decomposers, and heterotrophic bacteria. These heterogeneous assemblages of bacteria, by functional inference, have the potential to perform various ecological functions, i.e., cellulose degradation, cobalamin biosynthesis, fermentative hydrogen production, ammonium oxidation, amino acid fermentation, dissimilatory reduction of nitrate to ammonium, nitrite reduction, nitrate reduction, sulfur reduction, polyphosphate accumulation, denitrifying phosphorus-accumulation, and degradation of aromatic compounds. Results suggested that river populations of Cladophora provide ecologically important habitat for microorganisms that are key to nutrient cycling in lotic ecosystems.
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Affiliation(s)
- Karnjana Ruen-Pham
- Plants of Thailand Research Unit, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand;
| | - Linda E. Graham
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI 53706, USA;
| | - Anchittha Satjarak
- Plants of Thailand Research Unit, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand;
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23
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Song X, Song J, Yan Q, Zhou J, Cai Z. Assembly of a Benthic Microbial Community in a Eutrophic Bay with a Long History of Oyster Culturing. Microorganisms 2021; 9:microorganisms9102019. [PMID: 34683340 PMCID: PMC8536970 DOI: 10.3390/microorganisms9102019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 09/11/2021] [Accepted: 09/14/2021] [Indexed: 11/27/2022] Open
Abstract
The introduction of oysters to a waterbody is an efficient method for decreasing levels of eutrophication. Oysters affect sedimental environments and benthic microbes via their roles in nutrient cycling. However, little is known about how long-term oyster culturing affects benthic microbial community assembly. In the present study, top and bottom sediments from an oyster-culture area and non-culture area, in a eutrophic bay with a long history of oyster culturing, were obtained for environmental parameter measurement and microbe identification. Deterministic and stochastic processes in microbial community assembly were assessed. In particular, keystone species identification through network analysis was combined with measured environmental parameters to determine the factors related to community assembly processes. Our results suggest that oyster culturing relates to greater variation in both biological and non-biological sediment profiles. In benthic communities, Proteobacteria and Chloroflexi were the most abundant phyla, and community compositions were significantly different between sample groups. We also found that community assembly was more affected by deterministic factors than stochastic ones, when oysters were present. Moisture, or water content, and pH were identified as affecting deterministic and stochastic processes, respectively, but only water content was a driver associated with oyster culturing. Additionally, although keystone species presented a similar pattern of composition to peripheral species, they responded to their environments differently. Furthermore, model selection, fitting keystone species to community assembly processes, indicates their role in shaping microbial communities.
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Affiliation(s)
- Xiao Song
- School of Life Sciences, Tsinghua University, Beijing 100084, China; (X.S.); (J.S.); (Q.Y.)
- Shenzhen Public Platform of Screening and Application of Marine Microbial Resources, The Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China;
| | - Junting Song
- School of Life Sciences, Tsinghua University, Beijing 100084, China; (X.S.); (J.S.); (Q.Y.)
- Shenzhen Public Platform of Screening and Application of Marine Microbial Resources, The Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China;
| | - Qi Yan
- School of Life Sciences, Tsinghua University, Beijing 100084, China; (X.S.); (J.S.); (Q.Y.)
- Shenzhen Public Platform of Screening and Application of Marine Microbial Resources, The Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China;
| | - Jin Zhou
- Shenzhen Public Platform of Screening and Application of Marine Microbial Resources, The Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China;
| | - Zhonghua Cai
- Shenzhen Public Platform of Screening and Application of Marine Microbial Resources, The Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China;
- Correspondence:
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