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Rodríguez V, Bartholomäus A, Witzgall K, Riveras-Muñoz N, Oses R, Liebner S, Kallmeyer J, Rach O, Mueller CW, Seguel O, Scholten T, Wagner D. Microbial impact on initial soil formation in arid and semiarid environments under simulated climate change. Front Microbiol 2024; 15:1319997. [PMID: 38298893 PMCID: PMC10827993 DOI: 10.3389/fmicb.2024.1319997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 01/02/2024] [Indexed: 02/02/2024] Open
Abstract
The microbiota is attributed to be important for initial soil formation under extreme climate conditions, but experimental evidence for its relevance is scarce. To fill this gap, we investigated the impact of in situ microbial communities and their interrelationship with biocrust and plants compared to abiotic controls on soil formation in initial arid and semiarid soils. Additionally, we assessed the response of bacterial communities to climate change. Topsoil and subsoil samples from arid and semiarid sites in the Chilean Coastal Cordillera were incubated for 16 weeks under diurnal temperature and moisture variations to simulate humid climate conditions as part of a climate change scenario. Our findings indicate that microorganism-plant interaction intensified aggregate formation and stabilized soil structure, facilitating initial soil formation. Interestingly, microorganisms alone or in conjunction with biocrust showed no discernible patterns compared to abiotic controls, potentially due to water-masking effects. Arid soils displayed reduced bacterial diversity and developed a new community structure dominated by Proteobacteria, Actinobacteriota, and Planctomycetota, while semiarid soils maintained a consistently dominant community of Acidobacteriota and Proteobacteria. This highlighted a sensitive and specialized bacterial community in arid soils, while semiarid soils exhibited a more complex and stable community. We conclude that microorganism-plant interaction has measurable impacts on initial soil formation in arid and semiarid regions on short time scales under climate change. Additionally, we propose that soil and climate legacies are decisive for the present soil microbial community structure and interactions, future soil development, and microbial responses.
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Affiliation(s)
- Victoria Rodríguez
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Potsdam, Germany
| | | | - Kristina Witzgall
- Soil Science, TUM School of Life Sciences, Technical University of Munich, Freising-Weihenstephan, Germany
| | - Nicolás Riveras-Muñoz
- Department of Geosciences, Soil Science and Geomorphology, University of Tübingen, Tübingen, Germany
| | - Romulo Oses
- Centro Regional de Investigación y Desarrollo Sustentable de Atacama (CRIDESAT), Universidad de Atacama, Copiapó, Chile
| | - Susanne Liebner
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Potsdam, Germany
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Jens Kallmeyer
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Potsdam, Germany
| | - Oliver Rach
- GFZ German Research Centre for Geosciences, Section Geomorphology, Potsdam, Germany
| | - Carsten W. Mueller
- Institute for Ecology, Chair of Soil Science, Technische Universitaet Berlin, Berlin, Germany
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Copenhagen, Denmark
| | - Oscar Seguel
- Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago, Chile
| | - Thomas Scholten
- Department of Geosciences, Soil Science and Geomorphology, University of Tübingen, Tübingen, Germany
| | - Dirk Wagner
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Potsdam, Germany
- Institute of Geosciences, University of Potsdam, Potsdam, Germany
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Filippidou S, Price A, Spencer-Jones C, Scales A, Macey MC, Franchi F, Lebogang L, Cavalazzi B, Schwenzer SP, Olsson-Francis K. Diversity of Microbial Mats in the Makgadikgadi Salt Pans, Botswana. Microorganisms 2024; 12:147. [PMID: 38257974 PMCID: PMC10818877 DOI: 10.3390/microorganisms12010147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 12/19/2023] [Accepted: 12/22/2023] [Indexed: 01/24/2024] Open
Abstract
The Makgadikgadi Salt Pans are the remnants of a mega paleo-lake system in the central Kalahari, Botswana. Today, the Makgadikgadi Basin is an arid to semi-arid area receiving water of meteoric origin during the short, wet season. Large microbial mats, which support primary production, are formed due to desiccation during the dry season. This study aimed to characterise the microbial diversity of the microbial mats and the underlying sediment. The focus was the Ntwetwe Pan, located west of the Makgadikgadi Basin. Metagenomic analyses demonstrated that the mats consisted of a high relative abundance of Cyanobacteriota (synonym Cyanobacteria) (20.50-41.47%), Pseudomonadota (synonym Proteobacteria) (15.71 to 32.18%), and Actinomycetota (synonym Actinobacteria) (8.53-32.56%). In the underlying sediments, Pseudomonadota, Actinomycetota, and Euryarchaeota represented over 70% of the community. Localised fluctuations in water content and pH did not significantly affect the microbial diversity of the sediment or the mats.
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Affiliation(s)
- Sevasti Filippidou
- AstrobiologyOU, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes MK7 6AA, UK; (S.F.); (A.P.); (C.S.-J.); (A.S.); (M.C.M.); (S.P.S.)
- School of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Alex Price
- AstrobiologyOU, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes MK7 6AA, UK; (S.F.); (A.P.); (C.S.-J.); (A.S.); (M.C.M.); (S.P.S.)
| | - Charlotte Spencer-Jones
- AstrobiologyOU, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes MK7 6AA, UK; (S.F.); (A.P.); (C.S.-J.); (A.S.); (M.C.M.); (S.P.S.)
- Department of Geography, Durham University, Durham DH1 3LE, UK
| | - Anthony Scales
- AstrobiologyOU, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes MK7 6AA, UK; (S.F.); (A.P.); (C.S.-J.); (A.S.); (M.C.M.); (S.P.S.)
| | - Michael C. Macey
- AstrobiologyOU, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes MK7 6AA, UK; (S.F.); (A.P.); (C.S.-J.); (A.S.); (M.C.M.); (S.P.S.)
| | - Fulvio Franchi
- Earth and Environmental Science Department, Botswana International University of Science and Technology, Palapye 10071, Botswana;
- School of Geosciences, University of the Witwatersrand, Johannesburg 2001, South Africa
| | - Lesedi Lebogang
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Palapye 10071, Botswana;
| | - Barbara Cavalazzi
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, 40126 Bologna, Italy;
- Department of Geology, University of Johannesburg, Johannesburg 2006, South Africa
| | - Susanne P. Schwenzer
- AstrobiologyOU, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes MK7 6AA, UK; (S.F.); (A.P.); (C.S.-J.); (A.S.); (M.C.M.); (S.P.S.)
| | - Karen Olsson-Francis
- AstrobiologyOU, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes MK7 6AA, UK; (S.F.); (A.P.); (C.S.-J.); (A.S.); (M.C.M.); (S.P.S.)
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Li H, Zhang H, Li H, Duan L, Zhang X, Gao Y, Hall IR, Hemming SR, LeVay LJ. Sedimentary DNA reveals the link between microbial community dynamics and climate during the late last glaciation in the offshore region of the Zambezi River, Southwest Indian Ocean. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167787. [PMID: 37844644 DOI: 10.1016/j.scitotenv.2023.167787] [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: 06/29/2023] [Revised: 10/04/2023] [Accepted: 10/10/2023] [Indexed: 10/18/2023]
Abstract
Reconstructing the relationship between microbial communities and past abrupt climate change is of great importance for understanding current biodiversity patterns and predicting changes under future climate scenarios. However, little is currently known about how microbial communities respond to changes in key environmental stages due to a lack of research in this area. Here, we examine the variability in the communities of bacteria, archaea, and fungi from sediments deposited offshore region of the Zambezi River between 21.7 and 9.6 thousand years ago (ka) (covering the last glacial maximum, or LGM, and the early Holocene) using DNA metabarcoding approach via high-throughput sequencing. The results showed that (1) microbial assemblages differed across three key time intervals, with the last deglaciation having the most homogeneous prokaryotic assemblages, while for fungal communities in the LGM, and the early Holocene and LGM differing the most; (2) the warm early Holocene showed the highest diversity, whereas the lowest diversity was found in the LGM; and (3) the selected indicator species better reflected the climatic characteristics of different environmental stages. These results highlight the power of ancient sedimentary DNA to refine our understanding of microbial dynamics in marine sedimentary systems near large rivers, thus providing a basis for better modeling ecological processes in further research.
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Affiliation(s)
- Haoyu Li
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, 650500 Kunming, China
| | - Hucai Zhang
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, 650500 Kunming, China.
| | - Huayong Li
- School of Resource Environment and Tourism, Anyang Normal University, Anyang 455000, China
| | - Lizeng Duan
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, 650500 Kunming, China
| | - Xiaonan Zhang
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, 650500 Kunming, China
| | - Youhong Gao
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, 650500 Kunming, China
| | - Ian R Hall
- Department of Earth Sciences, Cardiff University, Main College, Park Place, PO Box 914, Cardiff, Wales CF10 3AT, United Kingdom
| | - Sidney R Hemming
- Lamont-Doherty Earth Observatory, Columbia University, 61 Route 9W, Palisades, NY, 10964, USA
| | - Leah J LeVay
- International Ocean Discovery Program, Texas A&M University, College Station, TX 77845, USA
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Martínez-Alvarez L, Ramond JB, Vikram S, León-Sobrino C, Maggs-Kölling G, Cowan DA. With a pinch of salt: metagenomic insights into Namib Desert salt pan microbial mats and halites reveal functionally adapted and competitive communities. Appl Environ Microbiol 2023; 89:e0062923. [PMID: 37971255 PMCID: PMC10734447 DOI: 10.1128/aem.00629-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 07/24/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE The hyperarid Namib Desert is one of the oldest deserts on Earth. It contains multiple clusters of playas which are saline-rich springs surrounded by halite evaporites. Playas are of great ecological importance, and their indigenous (poly)extremophilic microorganisms are potentially involved in the precipitation of minerals such as carbonates and sulfates and have been of great biotechnological importance. While there has been a considerable amount of microbial ecology research performed on various Namib Desert edaphic microbiomes, little is known about the microbial communities inhabiting its multiple playas. In this work, we provide a comprehensive taxonomic and functional potential characterization of the microbial, including viral, communities of sediment mats and halites from two distant salt pans of the Namib Desert, contributing toward a better understanding of the ecology of this biome.
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Affiliation(s)
- Laura Martínez-Alvarez
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics (CMEG), University of Pretoria, Pretoria, South Africa
| | - Jean-Baptiste Ramond
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics (CMEG), University of Pretoria, Pretoria, South Africa
- Extreme Ecosystem Microbiomics & Ecogenomics (E²ME) Lab., Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Surendra Vikram
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics (CMEG), University of Pretoria, Pretoria, South Africa
| | - Carlos León-Sobrino
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics (CMEG), University of Pretoria, Pretoria, South Africa
| | | | - Don A. Cowan
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics (CMEG), University of Pretoria, Pretoria, South Africa
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Aldeguer-Riquelme B, Antón J, Santos F. Distribution, abundance, and ecogenomics of the Palauibacterales, a new cosmopolitan thiamine-producing order within the Gemmatimonadota phylum. mSystems 2023; 8:e0021523. [PMID: 37345931 PMCID: PMC10469786 DOI: 10.1128/msystems.00215-23] [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: 03/05/2023] [Accepted: 04/19/2023] [Indexed: 06/23/2023] Open
Abstract
The phylum Gemmatimonadota comprises mainly uncultured microorganisms that inhabit different environments such as soils, freshwater lakes, marine sediments, sponges, or corals. Based on 16S rRNA gene studies, the group PAUC43f is one of the most frequently retrieved Gemmatimonadota in marine samples. However, its physiology and ecological roles are completely unknown since, to date, not a single PAUC43f isolate or metagenome-assembled genome (MAG) has been characterized. Here, we carried out a broad study of the distribution, abundance, ecotaxonomy, and metabolism of PAUC43f, for which we propose the name of Palauibacterales. This group was detected in 4,965 16S rRNA gene amplicon datasets, mainly from marine sediments, sponges, corals, soils, and lakes, reaching up to 34.3% relative abundance, which highlights its cosmopolitan character, mainly salt-related. The potential metabolic capabilities inferred from 52 Palauibacterales MAGs recovered from marine sediments, sponges, and saline soils suggested a facultative aerobic and chemoorganotrophic metabolism, although some members may also oxidize hydrogen. Some Palauibacterales species might also play an environmental role as N2O consumers as well as suppliers of serine and thiamine. When compared to the rest of the Gemmatimonadota phylum, the biosynthesis of thiamine was one of the key features of the Palauibacterales. Finally, we show that polysaccharide utilization loci (PUL) are widely distributed within the Gemmatimonadota so that they are not restricted to Bacteroidetes, as previously thought. Our results expand the knowledge about this cryptic phylum and provide new insights into the ecological roles of the Gemmatimonadota in the environment. IMPORTANCE Despite advances in molecular and sequencing techniques, there is still a plethora of unknown microorganisms with a relevant ecological role. In the last years, the mostly uncultured Gemmatimonadota phylum is attracting scientific interest because of its widespread distribution and abundance, but very little is known about its ecological role in the marine ecosystem. Here we analyze the global distribution and potential metabolism of the marine Gemmatimonadota group PAUC43f, for which we propose the name of Palauibacterales order. This group presents a saline-related character and a chemoorganoheterotrophic and facultatively aerobic metabolism, although some species might oxidize H2. Given that Palauibacterales is potentially able to synthesize thiamine, whose auxotrophy is the second most common in the marine environment, we propose Palauibacterales as a key thiamine supplier to the marine communities. This finding suggests that Gemmatimonadota could have a more relevant role in the marine environment than previously thought.
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Affiliation(s)
- Borja Aldeguer-Riquelme
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain
| | - Josefa Antón
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain
- Multidisciplinary Institute of Environmental Studies Ramón Margalef, University of Alicante, Alicante, Spain
| | - Fernando Santos
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain
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Chen M, Conroy JL, Sanford RA, Wyman-Feravich DA, Chee-Sanford JC, Connor LM. Tropical lacustrine sediment microbial community response to an extreme El Niño event. Sci Rep 2023; 13:6868. [PMID: 37106028 PMCID: PMC10140070 DOI: 10.1038/s41598-023-33280-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 04/11/2023] [Indexed: 04/29/2023] Open
Abstract
Salinity can influence microbial communities and related functional groups in lacustrine sediments, but few studies have examined temporal variability in salinity and associated changes in lacustrine microbial communities and functional groups. To better understand how microbial communities and functional groups respond to salinity, we examined geochemistry and functional gene amplicon sequence data collected from 13 lakes located in Kiritimati, Republic of Kiribati (2° N, 157° W) in July 2014 and June 2019, dates which bracket the very large El Niño event of 2015-2016 and a period of extremely high precipitation rates. Lake water salinity values in 2019 were significantly reduced and covaried with ecological distances between microbial samples. Specifically, phylum- and family-level results indicate that more halophilic microorganisms occurred in 2014 samples, whereas more mesohaline, marine, or halotolerant microorganisms were detected in 2019 samples. Functional Annotation of Prokaryotic Taxa (FAPROTAX) and functional gene results (nifH, nrfA, aprA) suggest that salinity influences the relative abundance of key functional groups (chemoheterotrophs, phototrophs, nitrogen fixers, denitrifiers, sulfate reducers), as well as the microbial diversity within functional groups. Accordingly, we conclude that microbial community and functional gene groups in the lacustrine sediments of Kiritimati show dynamic changes and adaptations to the fluctuations in salinity driven by the El Niño-Southern Oscillation.
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Affiliation(s)
- Mingfei Chen
- Department of Earth Science and Environmental Change, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Jessica L Conroy
- Department of Earth Science and Environmental Change, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Robert A Sanford
- Department of Earth Science and Environmental Change, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | | | - Joanne C Chee-Sanford
- Department of Natural Resource and Environmental Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- USDA-ARS, Urbana, IL, USA
| | - Lynn M Connor
- Department of Natural Resource and Environmental Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- USDA-ARS, Urbana, IL, USA
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Xiang X, Wang H, Man B, Xu Y, Gong L, Tian W, Yang H. Diverse Bathyarchaeotal Lineages Dominate Archaeal Communities in the Acidic Dajiuhu Peatland, Central China. MICROBIAL ECOLOGY 2023; 85:557-571. [PMID: 35332366 DOI: 10.1007/s00248-022-01990-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 03/06/2022] [Indexed: 06/14/2023]
Abstract
Bathyarchaeota are believed to have roles in the carbon cycle in marine systems. However, the ecological knowledge of Bathyarchaeota is limited in peatland ecosystems. Here, we investigated the vertical distribution of Bathyarchaeota community structure using quantitative PCR and high-throughput sequencing technology of ribosomal 16S rRNA gene integrated with detailed chemical profiling in the Dajiuhu Peatland, central China. Eight archaeal phyla were observed in peat samples, which mainly composed of Bathyarchaeota with a mean relative abundance about 88%, followed by Thaumarchaeota (9%). Bathyarchaeota were further split into 17 subgroups, and some subgroups showed habitat specificity to peat horizons with distinct lithological and physicochemical properties, for example, Bathy-6 and Bathy-15 had preference for the acrotelm, Bathy-5b, Bathy-16, and Bathy-19 were enriched in the catotelm, Bathy-5a, Bathy-8, and Bathy-11 were specific for the clay horizon. This spatial distribution pattern of archaeal communities along peat profile was mainly influenced by water content as indicated by RDA ordination and permutational MANOVA, whereas organic matter content exclusively affected Bathyarchaeota distribution along the peat profile significantly. The abundance of archaeal 16S rRNA genes ranged from 105 to 107 copies per gram dry sediment, and the highest archaeal biomass was observed in the periodically oxic mesotelm horizon with more dynamic archaeal interaction relationship as indicated by the network analysis. Bathyarchaeota dominated the archaeal interaction network with 82% nodes, 96% edges, and 71% keystone species. Our results provide an overview of the archaeal population, community structure, and relationship with environmental factors that affect the vertical distribution of archaeal communities and emphasize the ecology of bathyarchaeotal lineages in terrestrial peatland ecosystems.
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Affiliation(s)
- Xing Xiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074, Wuhan, China
- College of Life Science, Shangrao Normal University, Shangrao, 334001, China
- Hubei Key Laboratory of Critical Zone Evolution, China University of Geosciences, Wuhan, 430074, China
| | - Hongmei Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074, Wuhan, China.
| | - Baiying Man
- College of Life Science, Shangrao Normal University, Shangrao, 334001, China
| | - Ying Xu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074, Wuhan, China
| | - Linfeng Gong
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Third Institute of Oceanography, SOA, Xiamen, 361005, China
| | - Wen Tian
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074, Wuhan, China
| | - Huan Yang
- Hubei Key Laboratory of Critical Zone Evolution, China University of Geosciences, Wuhan, 430074, China
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Chaudhary DR, Kumar M, Kalla V. Sediment microbial community structure, enzymatic activities and functional gene abundance in the coastal hypersaline habitats. Arch Microbiol 2023; 205:56. [PMID: 36607455 DOI: 10.1007/s00203-022-03398-4] [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: 09/24/2022] [Revised: 12/20/2022] [Accepted: 12/30/2022] [Indexed: 01/07/2023]
Abstract
Salt marsh vegetation, mudflat and salt production are common features in worldwide coastal areas; however, their influence on microbial community composition and structure has been poorly studied and rarely compared. In the present study, microbial community composition (phospholipid fatty acid (PLFA) profiling and 16S rRNA gene sequencing (bacterial and archaeal)) and structure, enzymatic activities and abundance of functional genes in the sediments of salt ponds (crystallizer, condenser and reservoir), mudflat and vegetated mudflat were determined. Enzyme activities (β-glucosidase, urease and alkaline phosphatase) were considerably decreased in saltpan sediments because of elevated salinity while sediment of vegetated mudflat sediments showed the highest enzyme activities. Concentrations of total microbial biomarker PLFAs (total bacterial, Gram-positive, Gram-negative, fungal and actinomycetes) were the highest in vegetated mudflat sediments and the lowest in crystallizer sediments. Nonmetric-multidimensional scaling (NMDS) analysis of PLFA data revealed that the microbial community of crystallizer, mudflat and vegetated mudflat was significantly different from each other as well as different from condenser and reservoir. The most predominant phyla within the classified bacterial fractions were Proteobacteria followed by Firmicutes, Bacteroidetes and Planctomycetes, while Euryarchaeota and Crenarchaeota phyla dominated the classified archaeal fraction. Cyanobacterial genotypes were the most dominant in the condenser. Mudflat and vegetated mudflat supported a greater abundance of Bacteroidetes and Actinobacteria, respectively. The results of the present study suggest that salt ponds had significantly decreased the microbial and enzyme activities in comparison to mudflat and vegetated mudflat sediments due to very high salinity, ionic concentrations and devoid of vegetation. The present study expands our understanding of microbial resource utilization and adaptations of microorganisms in a hypersaline environment.
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Affiliation(s)
- Doongar R Chaudhary
- Division of Plant Omics, CSIR - Central Salt and Marine Chemicals Research Institute, G. B. Marg, Bhavnagar, Gujarat, 364002, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
| | - Madhav Kumar
- Division of Plant Omics, CSIR - Central Salt and Marine Chemicals Research Institute, G. B. Marg, Bhavnagar, Gujarat, 364002, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Vandana Kalla
- Lachoo Memorial College of Science and Technology, Shastri Nagar, Sec. A, Jodhpur, 342001, Rajasthan, India
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Abulaizi M, Chen M, Yang Z, Hu Y, Zhu X, Jia H. Response of soil bacterial community to alpine wetland degradation in arid Central Asia. FRONTIERS IN PLANT SCIENCE 2023; 13:990597. [PMID: 36684714 PMCID: PMC9848402 DOI: 10.3389/fpls.2022.990597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 11/25/2022] [Indexed: 06/17/2023]
Abstract
A large number of studies have reported the importance of bacterial communities in ecosystems and their responses to soil degradation, but the response mechanism in arid alpine wetlands is still unclear. Here, the non-degraded (ND), slightly degraded (SD), and heavily degraded (HD) regions of Bayinbuluk alpine wetland were used to analyzed the diversity, structure and function of bacterial communities in three degraded wetlands using 16S rRNA. The results showed that with the increase of degradation degree, the content of soil moisture (SM) and available nitrogen (AN) decreased significantly, plant species richness and total vegetation coverage decreased significantly, Cyperaceae (Cy) coverage decreased significantly, and Gramineae (Gr) coverage increased significantly. Degradation did not significantly affect the diversity of the bacterial community, but changed the relative abundance of the community structure. Degradation significantly increased the relative abundance of Actinobacteria (ND: 3.95%; SD: 7.27%; HD: 23.97%) and Gemmatimonadetes (ND: 0.39%; SD: 2.17%; HD: 10.78%), while significantly reducing the relative abundance of Chloroflexi (ND: 13.92%; SD: 8.68%; HD: 3.55%) and Nitrospirae (ND: 6.18%; SD: 0.45%; HD: 2.32%). Degradation significantly reduced some of the potential functions in the bacterial community associated with the carbon (C), nitrogen (N) and sulfur (S) cycles, such as hydrocarbon degradation (ND: 25.00%; SD: 1.74%; HD: 6.59%), such as aerobic ammonia oxidation (ND: 5.96%; SD: 22.82%; HD: 4.55%), and dark sulfide oxidation (ND: 32.68%; SD: 0.37%; HD: 0.28%). Distance-based redundancy analysis (db-RDA) results showed that the bacteria community was significantly related to the TC (total carbon) and Gr (P < 0.05). The results of linear discriminant analysis effect size (LEfSe) analysis indicate significant enrichments of Alphaproteobacteria and Sphingomonas in the HD area. The vegetation communities and soil nutrients changed significantly with increasing soil degradation levels, and Sphingomonas could be used as potential biomarker of degraded alpine wetlands.
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Affiliation(s)
- Maidinuer Abulaizi
- College of Resources and Environment, Xinjiang Agricultural University, Urumqi, China
| | - Mo Chen
- College of Grassland Science, Xinjiang Agricultural University, Urumqi, China
| | - Zailei Yang
- College of Resources and Environment, Xinjiang Agricultural University, Urumqi, China
| | - Yang Hu
- College of Resources and Environment, Xinjiang Agricultural University, Urumqi, China
| | - Xinping Zhu
- College of Resources and Environment, Xinjiang Agricultural University, Urumqi, China
- Xinjiang Key Laboratory of Soil and Plant Ecological Processes, Urumqi, China
| | - Hongtao Jia
- College of Resources and Environment, Xinjiang Agricultural University, Urumqi, China
- Xinjiang Key Laboratory of Soil and Plant Ecological Processes, Urumqi, China
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10
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Coskun ÖK, Gomez-Saez GV, Beren M, Ozcan D, Hosgormez H, Einsiedl F, Orsi WD. Carbon metabolism and biogeography of candidate phylum " Candidatus Bipolaricaulota" in geothermal environments of Biga Peninsula, Turkey. Front Microbiol 2023; 14:1063139. [PMID: 36910224 PMCID: PMC9992828 DOI: 10.3389/fmicb.2023.1063139] [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: 10/06/2022] [Accepted: 01/17/2023] [Indexed: 02/25/2023] Open
Abstract
Terrestrial hydrothermal springs and aquifers are excellent sites to study microbial biogeography because of their high physicochemical heterogeneity across relatively limited geographic regions. In this study, we performed 16S rRNA gene sequencing and metagenomic analyses of the microbial diversity of 11 different geothermal aquifers and springs across the tectonically active Biga Peninsula (Turkey). Across geothermal settings ranging in temperature from 43 to 79°C, one of the most highly represented groups in both 16S rRNA gene and metagenomic datasets was affiliated with the uncultivated phylum "Candidatus Bipolaricaulota" (former "Ca. Acetothermia" and OP1 division). The highest relative abundance of "Ca. Bipolaricaulota" was observed in a 68°C geothermal brine sediment, where it dominated the microbial community, representing 91% of all detectable 16S rRNA genes. Correlation analysis of "Ca. Bipolaricaulota" operational taxonomic units (OTUs) with physicochemical parameters indicated that salinity was the strongest environmental factor measured associated with the distribution of this novel group in geothermal fluids. Correspondingly, analysis of 23 metagenome-assembled genomes (MAGs) revealed two distinct groups of "Ca. Bipolaricaulota" MAGs based on the differences in carbon metabolism: one group encoding the bacterial Wood-Ljungdahl pathway (WLP) for H2 dependent CO2 fixation is selected for at lower salinities, and a second heterotrophic clade that lacks the WLP that was selected for under hypersaline conditions in the geothermal brine sediment. In conclusion, our results highlight that the biogeography of "Ca. Bipolaricaulota" taxa is strongly correlated with salinity in hydrothermal ecosystems, which coincides with key differences in carbon acquisition strategies. The exceptionally high relative abundance of apparently heterotrophic representatives of this novel candidate Phylum in geothermal brine sediment observed here may help to guide future enrichment experiments to obtain representatives in pure culture.
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Affiliation(s)
- Ömer K Coskun
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Gonzalo V Gomez-Saez
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany.,GeoBio-CenterLMU, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Murat Beren
- Department of Geological Engineering, Istanbul University-Cerrahpasa, Istanbul, Türkiye
| | - Dogacan Ozcan
- Department of Geological Engineering, Istanbul University-Cerrahpasa, Istanbul, Türkiye
| | - Hakan Hosgormez
- Department of Geological Engineering, Istanbul University-Cerrahpasa, Istanbul, Türkiye
| | - Florian Einsiedl
- Chair of Hydrogeology, TUM School of Engineering and Design, Technical University of Munich, Munich, Germany
| | - William D Orsi
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany.,GeoBio-CenterLMU, Ludwig-Maximilians-Universität München, Munich, Germany
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11
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Aldeguer-Riquelme B, Rubio-Portillo E, Álvarez-Rogel J, Giménez-Casalduero F, Otero XL, Belando MD, Bernardeau-Esteller J, García-Muñoz R, Forcada A, Ruiz JM, Santos F, Antón J. Factors structuring microbial communities in highly impacted coastal marine sediments (Mar Menor lagoon, SE Spain). Front Microbiol 2022; 13:937683. [PMID: 36160249 PMCID: PMC9491240 DOI: 10.3389/fmicb.2022.937683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/27/2022] [Indexed: 11/21/2022] Open
Abstract
Coastal marine lagoons are environments highly vulnerable to anthropogenic pressures such as agriculture nutrient loading or runoff from metalliferous mining. Sediment microorganisms, which are key components in the biogeochemical cycles, can help attenuate these impacts by accumulating nutrients and pollutants. The Mar Menor, located in the southeast of Spain, is an example of a coastal lagoon strongly altered by anthropic pressures, but the microbial community inhabiting its sediments remains unknown. Here, we describe the sediment prokaryotic communities along a wide range of environmental conditions in the lagoon, revealing that microbial communities were highly heterogeneous among stations, although a core microbiome was detected. The microbiota was dominated by Delta- and Gammaproteobacteria and members of the Bacteroidia class. Additionally, several uncultured groups such as Asgardarchaeota were detected in relatively high proportions. Sediment texture, the presence of Caulerpa or Cymodocea, depth, and geographic location were among the most important factors structuring microbial assemblages. Furthermore, microbial communities in the stations with the highest concentrations of potentially toxic elements (Fe, Pb, As, Zn, and Cd) were less stable than those in the non-contaminated stations. This finding suggests that bacteria colonizing heavily contaminated stations are specialists sensitive to change.
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Affiliation(s)
- Borja Aldeguer-Riquelme
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain
| | - Esther Rubio-Portillo
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain
| | - José Álvarez-Rogel
- Department of Agricultural Engineering of the Escuela Técnica Superior Ingeniería Agronómica (ETSIA) & Soil Ecology and Biotechnology Unit of the Institute of Plant Biotechnology, Technical University of Cartagena, Cartagena, Spain
| | | | - Xose Luis Otero
- Cross-Research in Environmental Technologies (CRETUS), Departamento de Edafoloxía e Química Agrícola, Facultade de Bioloxía, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - María-Dolores Belando
- Seagrass Ecology Group, Spanish Oceanography Institute of the Spanish National Research Council, Oceanography Center of Murcia, Murcia, Spain
| | - Jaime Bernardeau-Esteller
- Seagrass Ecology Group, Spanish Oceanography Institute of the Spanish National Research Council, Oceanography Center of Murcia, Murcia, Spain
| | - Rocío García-Muñoz
- Seagrass Ecology Group, Spanish Oceanography Institute of the Spanish National Research Council, Oceanography Center of Murcia, Murcia, Spain
| | - Aitor Forcada
- Department of Marine Science and Applied Biology, University of Alicante, Alicante, Spain
| | - Juan M. Ruiz
- Seagrass Ecology Group, Spanish Oceanography Institute of the Spanish National Research Council, Oceanography Center of Murcia, Murcia, Spain
| | - Fernando Santos
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain
| | - Josefa Antón
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain
- Multidisciplinary Institute of Environmental Studies Ramón Margalef, University of Alicante, Alicante, Spain
- *Correspondence: Josefa Antón,
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12
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Tu D, Ke J, Luo Y, Hong T, Sun S, Han J, Chen S. Microbial community structure and shift pattern of industry brine after a long-term static storage in closed tank. Front Microbiol 2022; 13:975271. [PMID: 36118215 PMCID: PMC9478951 DOI: 10.3389/fmicb.2022.975271] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 08/05/2022] [Indexed: 11/13/2022] Open
Abstract
Brine from Dingyuan Salt Mine (Anhui, China), an athalassohaline hypersaline environment formed in the early tertiary Oligocene, is used to produce table salt for hundreds of millions of people. However, halophiles preserved in this niche during deposition are still unknown. Here, we employed cultivation and high-throughput sequencing strategies to uncover the microbial community and its shift after a long-term storage in the brine collected from Dingyuan Salt Mine. High-throughput sequencing showed (1) in the fresh brine (2021), Cyanobium_stocktickerPCC-6307 spp. (8.46%), Aeromonas spp. (6.91%) and Pseudomonas spp. (4.71%) are the dominant species in bacteria while Natronomonas spp. (18.89%), Halapricum spp. (13.73%), and Halomicrobium spp. (12.35%) in archaea; (2) after a 3-year-storage, Salinibacter spp. (30.01%) and Alcanivorax spp. (14.96%) surpassed Cyanobium_stocktickerPCC-6307 spp. (8.46%) becoming the dominant species in bacteria; Natronomonas spp. are still the dominant species, while Halorientalis spp. (14.80%) outnumbered Halapricum spp. becoming the dominant species in archaea; (3) Alcanivorax spp. and Halorientalis spp. two hydrocarbons degrading microorganisms were enriched in the brine containing hydrocarbons. Cultivation using hypersaline nutrient medium (20% NaCl) combined with high-throughput 16S rRNA gene sequencing showed that (1) the biomass significantly increased while the species diversity sharply declined after a 3-year-storage; (2) Halorubrum spp. scarcely detected from the environment total stocktickerDNA were flourishing after cultivation using AS-168 or NOM medium; (3) twelve possible new species were revealed based on almost full-length 16S rRNA gene sequence similarity search. This study generally uncovered the microbial community and the dominant halophiles in this inland athalassohaline salt mine, and provided a new insight on the shift pattern of dominant halophiles during a long-term storage, which illustrated the shaping of microorganisms in the unique environment, and the adaptation of microbe to the specific environment.
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Affiliation(s)
- Demei Tu
- College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Juntao Ke
- College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Yuqing Luo
- College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Tao Hong
- College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Siqi Sun
- Anhui Jiaotianxiang Biological Technology Co., Ltd., Xuancheng, China
| | - Jing Han
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Shaoxing Chen
- College of Life Sciences, Anhui Normal University, Wuhu, China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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13
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Hu W, Hou Q, Delgado-Baquerizo M, Stegen JC, Du Q, Dong L, Ji M, Sun Y, Yao S, Gong H, Xiong J, Xia R, Liu J, Aqeel M, Akram MA, Ran J, Deng J. Continental-scale niche differentiation of dominant topsoil archaea in drylands. Environ Microbiol 2022; 24:5483-5497. [PMID: 35706137 DOI: 10.1111/1462-2920.16099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 06/07/2022] [Indexed: 11/26/2022]
Abstract
Archaea represent a diverse group of microorganisms often associated with extreme environments. However, an integrated understanding of biogeographical patterns of the specialist Haloarchaea and the potential generalist ammonia-oxidizing archaea (AOA) across large-scale environmental gradients remains limited. We hypothesize that niche differentiation determines their distinct distributions along environmental gradients. To test the hypothesis, we use a continental-scale research network including 173 dryland sites across northern China. Our results demonstrate that Haloarchaea and AOA dominate topsoil archaeal communities. As hypothesized, Haloarchaea and AOA show strong niche differentiation associated with two ecosystem types mainly found in China's drylands (i.e., deserts vs. grasslands), and they differ in the degree of habitat specialization. The relative abundance and richness of Haloarchaea are higher in deserts due to specialization to relatively high soil salinity and extreme climates, while those of AOA are greater in grassland soils. Our results further indicate a divergence in ecological processes underlying the segregated distributions of Haloarchaea and AOA. Haloarchaea are governed primarily by environmental-based processes while the more generalist AOA are assembled mostly via spatial-based processes. Our findings add to existing knowledge of large-scale biogeography of topsoil archaea, advancing our predictive understanding on changes in topsoil archaeal communities in a drier world. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Weigang Hu
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Qingqing Hou
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistemico. Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Av. Reina Mercedes 10, Sevilla, Spain.,Unidad Asociada CSIC-UPO (BioFun). Universidad Pablo de Olavide, Sevilla, Spain
| | - James C Stegen
- Ecosystem Science Team, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Qiajun Du
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Longwei Dong
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Mingfei Ji
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Yuan Sun
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Shuran Yao
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Haiyang Gong
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Junlan Xiong
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Rui Xia
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Jiayuan Liu
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Muhammad Aqeel
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Muhammad Adnan Akram
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China.,School of Economics, Lanzhou University, Lanzhou, China
| | - Jinzhi Ran
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Jianming Deng
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
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14
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Rodriguez V, Moskwa LM, Oses R, Kühn P, Riveras-Muñoz N, Seguel O, Scholten T, Wagner D. Impact of Climate and Slope Aspects on the Composition of Soil Bacterial Communities Involved in Pedogenetic Processes along the Chilean Coastal Cordillera. Microorganisms 2022; 10:microorganisms10050847. [PMID: 35630293 PMCID: PMC9143490 DOI: 10.3390/microorganisms10050847] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 04/13/2022] [Accepted: 04/16/2022] [Indexed: 02/04/2023] Open
Abstract
Soil bacteria play a fundamental role in pedogenesis. However, knowledge about both the impact of climate and slope aspects on microbial communities and the consequences of these items in pedogenesis is lacking. Therefore, soil-bacterial communities from four sites and two different aspects along the climate gradient of the Chilean Coastal Cordillera were investigated. Using a combination of microbiological and physicochemical methods, soils that developed in arid, semi-arid, mediterranean, and humid climates were analyzed. Proteobacteria, Acidobacteria, Chloroflexi, Verrucomicrobia, and Planctomycetes were found to increase in abundance from arid to humid climates, while Actinobacteria and Gemmatimonadetes decreased along the transect. Bacterial-community structure varied with climate and aspect and was influenced by pH, bulk density, plant-available phosphorus, clay, and total organic-matter content. Higher bacterial specialization was found in arid and humid climates and on the south-facing slope and was likely promoted by stable microclimatic conditions. The presence of specialists was associated with ecosystem-functional traits, which shifted from pioneers that accumulated organic matter in arid climates to organic decomposers in humid climates. These findings provide new perspectives on how climate and slope aspects influence the composition and functional capabilities of bacteria, with most of these capabilities being involved in pedogenetic processes.
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Affiliation(s)
- Victoria Rodriguez
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, 14473 Potsdam, Germany; (V.R.); (L.-M.M.)
| | - Lisa-Marie Moskwa
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, 14473 Potsdam, Germany; (V.R.); (L.-M.M.)
| | - Rómulo Oses
- Centro Regional de Investigación y Desarrollo Sustentable de Atacama, Universidad de Atacama (CRIDESAT UDA), Copayapu 484, Copiapó 1530000, Chile;
| | - Peter Kühn
- Department of Geosciences, Soil Science and Geomorphology, University of Tübingen, 72070 Tübingen, Germany; (P.K.); (N.R.-M.); (T.S.)
| | - Nicolás Riveras-Muñoz
- Department of Geosciences, Soil Science and Geomorphology, University of Tübingen, 72070 Tübingen, Germany; (P.K.); (N.R.-M.); (T.S.)
| | - Oscar Seguel
- Facultad de Ciencias Agronómicas, Universidad de Chile, Av. Santa Rosa #11315, La Pintana, Santiago 8820808, Chile;
| | - Thomas Scholten
- Department of Geosciences, Soil Science and Geomorphology, University of Tübingen, 72070 Tübingen, Germany; (P.K.); (N.R.-M.); (T.S.)
| | - Dirk Wagner
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, 14473 Potsdam, Germany; (V.R.); (L.-M.M.)
- Institute of Geosciences, University of Potsdam, 14476 Potsdam, Germany
- Correspondence:
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15
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High Proportions of Radiation-Resistant Strains in Culturable Bacteria from the Taklimakan Desert. BIOLOGY 2022; 11:biology11040501. [PMID: 35453702 PMCID: PMC9030528 DOI: 10.3390/biology11040501] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 03/19/2022] [Accepted: 03/23/2022] [Indexed: 12/18/2022]
Abstract
Simple Summary Radiation-resistant extremophiles have frequently been found in the Taklimakan Desert, which is known for its harsh conditions. However, there is no systemic study investigating the diversity and proportion of radiation-resistant strains among culturable bacteria. The results of this study revealed the distribution of culturable bacteria in the Taklimakan Desert and indicated high proportions of radiation-resistant strains in the culturable bacteria. The study helps to better understand the ecological origin of radio-resistance and to quantitatively describe the desert as a common habitat for radiation-resistant extremophiles. Abstract The Taklimakan Desert located in China is the second-largest shifting sand desert in the world and is known for its harsh conditions. Types of γ-rays or UV radiation-resistant bacterial strains have been isolated from this desert. However, there is no information regarding the proportions of the radiation-resistant strains in the total culturable microbes. We isolated 352 bacterial strains from nine sites across the Taklimakan Desert from north to south. They belong to Actinobacteria, Firmicutes, Proteobacteria, and Bacteroidetes. The phylum Actinobacteria was the most predominant in abundance and Firmicutes had the highest species richness. Bacteroidetes had the lowest abundance and was found in four sites only, while the other three phyla were found in every site but with different distribution profiles. After irradiating with 1000 J/m2 and 6000 J/m2 UV-C, the strains with survival rates higher than 10% occupied 72.3% and 36.9% of all culturable bacteria, respectively. The members from Proteobacteria had the highest proportions, with survival rates higher than 10%. After radiation with 10 kGy γ-rays, Kocuria sp. TKL1057 and Planococcus sp. TKL1152 showed higher radiation-resistant capabilities than Deinococcus radiodurans R1. Besides obtaining several radiation-resistant extremophiles, this study measured the proportions of the radiation-resistant strains in the total culturable microbes for the first time. This study may help to better understand the origin of radioresistance, especially by quantitatively comparing proportions of radiation-resistant extremophiles from different environments in the future.
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16
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Lv J, Niu Y, Yuan R, Wang S. Different Responses of Bacterial and Archaeal Communities in River Sediments to Water Diversion and Seasonal Changes. Microorganisms 2021; 9:microorganisms9040782. [PMID: 33917984 PMCID: PMC8068392 DOI: 10.3390/microorganisms9040782] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 04/06/2021] [Accepted: 04/07/2021] [Indexed: 11/16/2022] Open
Abstract
In recent years, different responses of archaea and bacteria to environmental changes have attracted increasing scientific interest. In the mid-latitude region, Fen River receives water transferred from the Yellow River, electrical conductivity (EC), concentrations of Cl- and Na+ in water, total phosphorus (TP), and Olsen phosphorus (OP) in sediments were significantly affected by water transfer. Meanwhile, temperature and oxidation-reduction potential (ORP) of water showed significant seasonal variations. Based on 16S rRNA high-throughput sequencing technology, the composition of bacteria and archaea in sediments was determined in winter and summer, respectively. Results showed that the dominance of bacterial core flora decreased and that of archaeal core flora increased after water diversion. The abundance and diversity of bacterial communities in river sediments were more sensitive to anthropogenic and naturally induced environmental changes than that of archaeal communities. Bacterial communities showed greater resistance than archaeal communities under long-term external disturbances, such as seasonal changes, because of rich species composition and complex community structure. Archaea were more stable than bacteria, especially under short-term drastic environmental disturbances, such as water transfer, due to their insensitivity to environmental changes. These results have important implications for understanding the responses of bacterial and archaeal communities to environmental changes in river ecosystems affected by water diversion.
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Affiliation(s)
- Jiali Lv
- School of Environment and Natural Resources, Shanxi University, Taiyuan 030006, China; (J.L.); (Y.N.)
- Key Laboratory of Agricultural Water Resources Research, Innovation Academy for Seed Design, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China;
- Sino-Danish College of University of Chinese Academy of Sciences, Beijing 101408, China
| | - Yangdan Niu
- School of Environment and Natural Resources, Shanxi University, Taiyuan 030006, China; (J.L.); (Y.N.)
| | - Ruiqiang Yuan
- School of Environment and Natural Resources, Shanxi University, Taiyuan 030006, China; (J.L.); (Y.N.)
- Correspondence:
| | - Shiqin Wang
- Key Laboratory of Agricultural Water Resources Research, Innovation Academy for Seed Design, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China;
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17
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Genderjahn S, Lewin S, Horn F, Schleicher AM, Mangelsdorf K, Wagner D. Living Lithic and Sublithic Bacterial Communities in Namibian Drylands. Microorganisms 2021; 9:235. [PMID: 33498742 PMCID: PMC7911874 DOI: 10.3390/microorganisms9020235] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 01/17/2021] [Accepted: 01/20/2021] [Indexed: 12/26/2022] Open
Abstract
Dryland xeric conditions exert a deterministic effect on microbial communities, forcing life into refuge niches. Deposited rocks can form a lithic niche for microorganisms in desert regions. Mineral weathering is a key process in soil formation and the importance of microbial-driven mineral weathering for nutrient extraction is increasingly accepted. Advances in geobiology provide insight into the interactions between microorganisms and minerals that play an important role in weathering processes. In this study, we present the examination of the microbial diversity in dryland rocks from the Tsauchab River banks in Namibia. We paired culture-independent 16S rRNA gene amplicon sequencing with culture-dependent (isolation of bacteria) techniques to assess the community structure and diversity patterns. Bacteria isolated from dryland rocks are typical of xeric environments and are described as being involved in rock weathering processes. For the first time, we extracted extra- and intracellular DNA from rocks to enhance our understanding of potentially rock-weathering microorganisms. We compared the microbial community structure in different rock types (limestone, quartz-rich sandstone and quartz-rich shale) with adjacent soils below the rocks. Our results indicate differences in the living lithic and sublithic microbial communities.
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Affiliation(s)
- Steffi Genderjahn
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany; (S.L.); (F.H.); (D.W.)
| | - Simon Lewin
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany; (S.L.); (F.H.); (D.W.)
| | - Fabian Horn
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany; (S.L.); (F.H.); (D.W.)
| | - Anja M. Schleicher
- GFZ German Research Centre for Geosciences, Section Organic Geochemistry, Telegrafenberg, 14473 Potsdam, Germany;
| | - Kai Mangelsdorf
- GFZ German Research Centre for Geosciences, Section Anorganic Chemistry, Telegrafenberg, 14473 Potsdam, Germany;
| | - Dirk Wagner
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany; (S.L.); (F.H.); (D.W.)
- Institute of Geosciences, University of Potsdam, 14476 Potsdam, Germany
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18
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Wang H, Zeng Y, Guo C, Zheng X, Ding C, Lu G, Dang Z. Soil rehabilitation shaped different patterns of bacterial and archaeal community in AMD-irrigated paddy soil. CHEMOSPHERE 2021; 263:128259. [PMID: 33297204 DOI: 10.1016/j.chemosphere.2020.128259] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/28/2020] [Accepted: 09/01/2020] [Indexed: 06/12/2023]
Abstract
Microorganisms are essential for soil rehabilitation and long-term sustainability of established plants. However, the recovery process of microorganisms in AMD-irrigated paddy soil is poorly understood at present. To verify this, we sampled AMD-irrigated paddy soils before at different rehabilitation stages by characterizing bacteria and archaea community from a chronosequence of AMD-irrigated rehabilitation to pre-disturbance levels from references sites. Next-generation sequencing is used to describe shifts in diversity and taxonomic composition of bacterial and archaeal. Co-occurrence networks are constructed to reveal potential microbial interaction patterns. The result showed bacterial community followed an observable taxonomic transition overtimes, with community structure becoming more similar to that of unmined reference sites. But the archaeal community only showed a seasonal change, which may hint that the archaeal community needs more time in rehabilitation. Both bacterial and archaeal community composition changes were apparent at high taxonomic levels, bacterial communities become dominated by Proteobacteria phylum, and archaeal community was dominated by Crenarchaeota, we proposed the possible reason is bacterial community were mainly derived by soil pH while the archaeal community was impacted by heavy metal. The bacterial co-occurrence networks increased in complexity during succession, improving the community's resistance to environmental disturbance, while the archaeal did not change monotonically with time. This study highlights the distinct recovery pattern of the bacterial and archaeal community during AMD-irrigated paddy soil rehabilitation, which provides a deep understanding of their role in paddy soil, and subsequent harnessing of their potential to pave the way in future rehabilitation strategies for mined sites.
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Affiliation(s)
- Han Wang
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, PR China; State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, PR China
| | - Yufei Zeng
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, PR China
| | - Chuling Guo
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, PR China; The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, South China University of Technology, Guangzhou, 510006, PR China.
| | - Xiongkai Zheng
- School of Environmental Science and Engineering, Zhongkai University of Agriculture and Engineering, Guangzhou, 510006, PR China
| | - Cui Ding
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, PR China
| | - Guining Lu
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, PR China; The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, South China University of Technology, Guangzhou, 510006, PR China
| | - Zhi Dang
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, PR China; The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, South China University of Technology, Guangzhou, 510006, PR China
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19
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Lavrentyeva EV, Erdyneeva EB, Banzaraktsaeva TG, Kotsyurbenko OR, Baturina OA, Khakhinov VV, Kozyreva LP. Prokaryotic Diversity in the Biotopes of the Gudzhirganskoe Saline Lake (Barguzin Valley, Russia). Microbiology (Reading) 2020. [DOI: 10.1134/s0026261720030157] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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20
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Lee AH, Lee J, Hong S, Kwon BO, Xie Y, Giesy JP, Zhang X, Khim JS. Integrated assessment of west coast of South Korea by use of benthic bacterial community structure as determined by eDNA, concentrations of contaminants, and in vitro bioassays. ENVIRONMENT INTERNATIONAL 2020; 137:105569. [PMID: 32078869 DOI: 10.1016/j.envint.2020.105569] [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: 10/14/2019] [Revised: 01/24/2020] [Accepted: 02/09/2020] [Indexed: 06/10/2023]
Abstract
During the past few decades, contamination of sediments by persistent toxic substances (PTSs) has been observed in estuarine and coastal areas on the west coast of South Korea. The contaminants are suspected to cause toxicities in aquatic biota, but little is known about their ecological effects, particularly on benthic microbial communities. In this study, an eDNA-based assessment was applied along with classic assessments of exposure, such as chemistry and in vitro bioassays, to evaluate condition of benthic bacterial communities subjected to PTSs. Two strategies were adopted for the study. One was to conduct a comprehensive assessment in space (by comparing seawater and freshwater sites at five coastal regions) and in time (by following change over a 5-y period). Although we found that bacterial composition varied among and within years, some phyla, such as Proteobacteria (28.7%), Actinobacteria (13.1%), Firmicutes (12.7%), and Chloroflexi (12.5%) were consistently dominated across the study regions. Certain bacterial groups, such as Firmicutes and Verrucomicrobia have been linked to contamination at some sites in the study area and at specific points in time. Bacterial communities were not significantly correlated with salinity or AhR- and ER-mediated potencies, whereas concentrations of PAHs, APs, and certain metals (Cd and Hg) exhibited significant associations to the structure of bacterial communities at the phylum level. In fact, the relative abundance of microbes in the phylum Planctomycetes was significantly and negatively correlated with concentrations of PAHs and metals. Thus, the relative abundance of Planctomycetes could be used as an indicator of sedimentary contamination by PAHs and/or metals. Based on our correlation analyses, Cd and ER-mediated potencies were associated more with bacterial abundances at the class taxonomic level than were other PTSs and metals. Overall, the eDNA-based assessment was useful by augmenting more traditional measures of exposure and responses in a sediment triad approach and has potential as a more rapid screening tool.
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Affiliation(s)
- Aslan Hwanhwi Lee
- School of Earth and Environmental Sciences & Research Institute of Oceanography, Seoul National University, Seoul 08826, Republic of Korea.
| | - Junghyun Lee
- School of Earth and Environmental Sciences & Research Institute of Oceanography, Seoul National University, Seoul 08826, Republic of Korea.
| | - Seongjin Hong
- Department of Ocean Environmental Sciences, Chungnam National University, Daejeon 34134, Republic of Korea.
| | - Bong-Oh Kwon
- School of Earth and Environmental Sciences & Research Institute of Oceanography, Seoul National University, Seoul 08826, Republic of Korea.
| | - Yuwei Xie
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing 210003, China; Department of Veterinary Biomedical Sciences & Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada.
| | - John P Giesy
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing 210003, China; Department of Veterinary Biomedical Sciences & Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada; Department of Environmental Sciences, Baylor University, Waco, TX, USA; Department of Zoology and Center for Integrative Toxicology, Michigan State University, East Lansing, MI, USA.
| | - Xiaowei Zhang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing 210003, China.
| | - Jong Seong Khim
- School of Earth and Environmental Sciences & Research Institute of Oceanography, Seoul National University, Seoul 08826, Republic of Korea.
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21
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Feeding Formula Eliminates the Necessity of Bacterial Dysbiosis and Induces Inflammation and Injury in the Paneth Cell Disruption Murine NEC Model in an Osmolality-Dependent Manner. Nutrients 2020; 12:nu12040900. [PMID: 32224880 PMCID: PMC7230818 DOI: 10.3390/nu12040900] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 03/19/2020] [Accepted: 03/24/2020] [Indexed: 01/08/2023] Open
Abstract
Necrotizing enterocolitis (NEC) remains a significant cause of morbidity and mortality in preterm infants. Formula feeding is a risk factor for NEC and osmolality, which is increased by the fortification that is required for adequate growth of the infant, has been suggested as a potential cause. Our laboratory has shown that Paneth cell disruption followed by induction of dysbiosis can induce NEC-like pathology in the absence of feeds. We hypothesized adding formula feeds to the model would exacerbate intestinal injury and inflammation in an osmolality-dependent manner. NEC-like injury was induced in 14-16 day-old C57Bl/6J mice by Paneth cell disruption with dithizone or diphtheria toxin, followed by feeding rodent milk substitute with varying osmolality (250-1491 mOsm/kg H2O). Animal weight, serum cytokines and osmolality, small intestinal injury, and cecal microbial composition were quantified. Paneth cell-disrupted mice fed formula had significant NEC scores compared to controls and no longer required induction of bacterial dysbiosis. Significant increases in serum inflammatory markers, small intestinal damage, and overall mortality were osmolality-dependent and not related to microbial changes. Overall, formula feeding in combination with Paneth cell disruption induced NEC-like injury in an osmolality-dependent manner, emphasizing the importance of vigilance in designing preterm infant feeds.
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22
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Lee H, Heo YM, Kwon SL, Yoo Y, Lee AH, Kwon BO, Kim GH, Khim JS, Kim JJ. Recovery of the benthic bacterial community in coastal abandoned saltern requires over 35 years: A comparative case study in the Yellow Sea. ENVIRONMENT INTERNATIONAL 2020; 135:105412. [PMID: 31865277 DOI: 10.1016/j.envint.2019.105412] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 11/04/2019] [Accepted: 12/10/2019] [Indexed: 06/10/2023]
Abstract
Salt is an essential nutrient for humans, and salterns exist worldwide. Although the construction of salterns has stopped and typical salterns are now mostly abandoned, there has been no research on the ecological recovery of the abandoned salterns. Here, we analyzed the bacterial diversity and community structure in three pairs of abandoned salterns that have undergone 1-35 years of natural restoration and tidal flats to determine the recovery time and process. Partial 16S rRNA sequences were amplified and sequenced to investigate the biodiversity and structure of the bacterial community in sediments collected from abandoned salterns and adjacent natural tidal flats (viz., controls) in the Yellow Sea. The most abundant microorganisms across locations were found to be members of Proteobacteria, ranging from 45 to 72%, which was also a crucial taxon in the bacterial recovery process. The benthic bacterial community of the salterns showed time-dependent recovery, as demonstrated by the similarity between the salterns and controls. Indeed, dissimilarities between bacterial communities were significant for the saltern that had been abandoned for one year, according to ANOSIM (R = 1.0, p < 0.01). The genera that were determined to contribute to the dissimilarity exhibited a significant correlation with the sedimentary phosphorus concentration. The dataset generally supported that the indigenous benthic bacterial community in an altered marine environment might require a considerable time to return to a natural status. Meanwhile, a delay between the recovery of the physicochemical environment and biological component was evidenced, which seemed to influence the recovery time in a site-specific manner. Overall, the present study provided new insight and understanding of the recovery of the benthic bacterial community in abandoned salterns in terms of recovery time and the associated process.
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Affiliation(s)
- Hanbyul Lee
- Division of Environmental Science & Ecological Engineering, College of Life Science & Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Young Mok Heo
- Division of Environmental Science & Ecological Engineering, College of Life Science & Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Sun Lul Kwon
- Division of Environmental Science & Ecological Engineering, College of Life Science & Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Yeonjae Yoo
- Division of Environmental Science & Ecological Engineering, College of Life Science & Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Aslan Hwanhwi Lee
- School of Earth and Environmental Sciences & Research Institute of Oceanography, Seoul National University, Seoul 08826, Republic of Korea
| | - Bong-Oh Kwon
- School of Earth and Environmental Sciences & Research Institute of Oceanography, Seoul National University, Seoul 08826, Republic of Korea
| | - Gyu-Hyeok Kim
- Division of Environmental Science & Ecological Engineering, College of Life Science & Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Jong Seong Khim
- School of Earth and Environmental Sciences & Research Institute of Oceanography, Seoul National University, Seoul 08826, Republic of Korea.
| | - Jae-Jin Kim
- Division of Environmental Science & Ecological Engineering, College of Life Science & Biotechnology, Korea University, Seoul 02841, Republic of Korea.
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23
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Comparative evaluation of three archaeal primer pairs for exploring archaeal communities in deep-sea sediments and permafrost soils. Extremophiles 2019; 23:747-757. [PMID: 31489482 DOI: 10.1007/s00792-019-01128-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 08/27/2019] [Indexed: 10/26/2022]
Abstract
16S rRNA gene profiling is a powerful method for characterizing microbial communities; however, no universal primer pair can target all bacteria and archaea, resulting in different primer pairs which may impact the diversity profile obtained. Here, we evaluated three pairs of high-throughput sequencing primers for characterizing archaeal communities from deep-sea sediments and permafrost soils. The results show that primer pair Arch519/Arch915 (V4-V5 regions) produced the highest alpha diversity estimates, followed by Arch349f/Arch806r (V3-V4 regions) and A751f/AU1204r (V5-V7 regions) in both sample types. The archaeal taxonomic compositions and the relative abundance estimates of archaeal communities are influenced by the primer pairs. Beta diversity of the archaeal community detected by the three primer pairs reveals that primer pairs Arch349f/Arch806r and Arch519f/Arch915r are biased toward detection of Halobacteriales, Methanobacteriales and MBG-E/Hydrothermarchaeota, whereas the primer pairs Arch519f/Arch915r and A751f/UA1204r are biased to detect MBG-B/Lokiarchaeota, and the primers pairs Arch349f/Arch806r and A751f/UA1204r are biased to detect Methanomicrobiales and Methanosarcinales. The data suggest that the alpha and beta diversities of archaeal communities as well as the community compositions are influenced by the primer pair choice. This finding provides researchers with valuable experimental insight for selection of appropriate archaeal primer pairs to characterize archaeal communities.
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Nasir F, Shi S, Tian L, Chang C, Ma L, Li X, Gao Y, Tian C. Strigolactones shape the rhizomicrobiome in rice (Oryza sativa). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 286:118-133. [PMID: 31300137 DOI: 10.1016/j.plantsci.2019.05.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 05/13/2019] [Accepted: 05/18/2019] [Indexed: 05/03/2023]
Abstract
The rhizomicrobiome helps the host plant to better adapt to environmental stresses. In contrast, plant-derived metabolic substances, including phytohormones, play an active role in structuring rhizomicrobiome. Although strigolactones (SLs), a group of phytohormones, serve as potential rhizosphere signaling molecules, their contributions in shaping the rice (Oryza sativa) rhizomicrobiome remain elusive. To address this issue, we compared the rhizomicrobiome of rice mutants defective in either SL biosynthesis or signaling and wild-type (WT) plants. To understand whether SL-regulated metabolic pathways shape the rhizomicrobiome, a correlation network analysis was conducted among the metabolic pathway-related genes and the rhizomicrobiome of rice. Compared to WT, higher bacterial richness (evidenced by the operational taxonomic unit richness) and lower fungal diversity (evidenced by the Shannon index) were observed in both SL deficient dwarf17 (d17) and signaling (d14) mutants. Additionally, remarkable differences were observed in the composition of a large number of bacterial communities than the fungal communities in the d17 and d14 mutants with respect to the WT. The abundance of certain beneficial bacterial taxa, including Nitrosomonadaceae and Rhodanobacter, were significantly decreased in both mutants relative to the WT. Correlation network analysis between SL-regulated metabolic pathway-associated genes and rhizomicrobiome proposed a role for SL-dependent metabolic pathways in shaping rhizomicrobiome composition. Taken together, our study suggests that SL biosynthesis and signaling play a key role in determining the rice rhizomicrobiome, directly or indirectly, through the mediation of distinct metabolic pathways. Based on our findings, the genetic modulation of rice SL biosynthesis and/or signaling pathways may help to recruit/increase the abundance of the desired rhizomicrobiome, which may assist in the stress resilience of rice.
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Affiliation(s)
- Fahad Nasir
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, Jilin Province, China; Key Laboratory of Vegetation Ecology, Ministry of Education, Institute of Grassland Science, Northeast Normal University, Changchun 130024, Jilin Province, China
| | - Shaohua Shi
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, Jilin Province, China
| | - Lei Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, Jilin Province, China
| | - Chunling Chang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, Jilin Province, China
| | - Lina Ma
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, Jilin Province, China
| | - Xiujun Li
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, Jilin Province, China
| | - Yingzhi Gao
- Key Laboratory of Vegetation Ecology, Ministry of Education, Institute of Grassland Science, Northeast Normal University, Changchun 130024, Jilin Province, China.
| | - Chunjie Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, Jilin Province, China.
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25
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Liu BB, Narsing Rao MP, Yin XQ, Li X, Salam N, Zhang Y, Alkhalifah DHM, Hozzein WN, Li WJ. Description of Halegenticoccus soli gen. nov., sp. nov., a halophilic archaeon isolated from a soil sample of Ebi lake. Extremophiles 2019; 23:521-528. [PMID: 31147835 DOI: 10.1007/s00792-019-01104-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 05/21/2019] [Indexed: 10/26/2022]
Abstract
Two extreme halophilic archaeal strains, SYSUA9-0T and SYSUA9-1, were isolated from Ebi lake of Xinjiang, China. The colonies were Gram-negative, coccoid, and non-motile. Strains were aerobic and grew at 25-50 °C (optimum at 37 °C), in the presence of 10-35% (w/v) NaCl (optimum at 20-22%), and pH 6.0-8.0 (optimum at 7.0). The 16S rRNA gene sequence result revealed that the two strains were closely related to Haloprofundus marisrubri SB9T (92.7% similarity). The DNA-DNA hybridization value (97% ± 1%) suggested that SYSUA9-0T and SYSUA9-1 were similar; however, their sequence similarities with other archaeal members suggested that they were novel candidates. The genomic G + C content of SYSUA9-0T was 66.9%. The average nucleotide identity value between SYSU A9-0T and Haloprofundus marisrubri SB9T was 69.1%, which was far below the cutoff value (95-96%) proposed to define the species boundary. The polar lipids were phosphatidylglycerol (PG), phosphatidylglycerolphosphate methylester (PGP-Me), sulfated mannosyl glucosyl diether, mannosyl glucosyldiether, and four unidentified glycolipids. Phenotypic, chemotaxonomic and comparative genome analysis suggested that SYSU A9-0T and SYSU A9-1 represent a novel species of a new genus within the family Haloferacaceae, for which the name Halegenticoccus soli gen. nov., sp. nov., is proposed. The type strain is SYAUA9-0T (= KCTC4241T = CGMCC 1.15765T).
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Affiliation(s)
- Bing-Bing Liu
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, College of Biological and Chemical Engineering, Nanyang Institute of Technology, Nanyang, 473004, People's Republic of China
| | - Manik Prabhu Narsing Rao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Xiao-Qing Yin
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Xin Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Nimaichand Salam
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Yao Zhang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Dalal Hussien M Alkhalifah
- Biology Department, Faculty of Science, Princess Nourah Bint Abdulrahman University, Riyadh, 11564, Kingdom of Saudi Arabia
| | - Wael N Hozzein
- Bioproducts Research Chair, Zoology Department, College of Science, King Saud University, Riyadh, 11451, Kingdom of Saudi Arabia.,Botany and Microbiology Department, Faculty of Science, Beni-Suef University, Beni-Suef, Egypt
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China. .,Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürűmqi, 830011, China.
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