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de Santana CO, Spealman P, Oliveira E, Gresham D, de Jesus T, Chinalia F. Prokaryote communities along a source-to-estuary river continuum in the Brazilian Atlantic Forest. PeerJ 2024; 12:e17900. [PMID: 39157765 PMCID: PMC11328836 DOI: 10.7717/peerj.17900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 07/20/2024] [Indexed: 08/20/2024] Open
Abstract
The activities of microbiomes in river sediments play an important role in sustaining ecosystem functions by driving many biogeochemical cycles. However, river ecosystems are frequently affected by anthropogenic activities, which may lead to microbial biodiversity loss and/or changes in ecosystem functions and related services. While parts of the Atlantic Forest biome stretching along much of the eastern coast of South America are protected by governmental conservation efforts, an estimated 89% of these areas in Brazil are under threat. This adds urgency to the characterization of prokaryotic communities in this vast and highly diverse biome. Here, we present prokaryotic sediment communities in the tropical Juliana River system at three sites, an upstream site near the river source in the mountains (Source) to a site in the middle reaches (Valley) and an estuarine site near the urban center of Ituberá (Mangrove). The diversity and composition of the communities were compared at these sites, along with environmental conditions, the former by using qualitative and quantitative analyses of 16S rRNA gene amplicons. While the communities included distinct populations at each site, a suite of core taxa accounted for the majority of the populations at all sites. Prokaryote diversity was highest in the sediments of the Mangrove site and lowest at the Valley site. The highest number of genera exclusive to a given site was found at the Source site, followed by the Mangrove site, which contained some archaeal genera not present at the freshwater sites. Copper (Cu) concentrations were related to differences in communities among sites, but none of the other environmental factors we determined was found to have a significant influence. This may be partly due to an urban imprint on the Mangrove site by providing organic carbon and nutrients via domestic effluents.
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Affiliation(s)
- Carolina O. de Santana
- Department of Exact Sciences (DEXA), Universidade Estadual de Feira de Santana, Feira de Santana, Bahia, Brazil
| | - Pieter Spealman
- Department of Biology, New York University, New York City, NY, United States
| | - Eddy Oliveira
- Department of Biology (DCBIO), Universidade Estadual de Feira de Santana, Feira de Santana, BA, Brazil
| | - David Gresham
- Department of Biology, New York University, New York City, NY, United States
| | - Taise de Jesus
- Department of Exact Sciences (DEXA), Universidade Estadual de Feira de Santana, Feira de Santana, Bahia, Brazil
| | - Fabio Chinalia
- Institute of Health Sciences, Laboratory of Biotechnology and Ecology of Micro-Organisms, Institute of Health Sciences, Salvador, BA, Brazil
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Jiao F, Qian L, Wu J, Zhang D, Zhang J, Wang M, Sui X, Zhang X. Diversity and Composition of Soil Acidobacterial Communities in Different Temperate Forest Types of Northeast China. Microorganisms 2024; 12:963. [PMID: 38792792 PMCID: PMC11124458 DOI: 10.3390/microorganisms12050963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 05/05/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
To gain an in-depth understanding of the diversity and composition of soil Acidobacteria in five different forest types in typical temperate forest ecosystems and to explore their relationship with soil nutrients. The diversity of soil Acidobacteria was determined by high-throughput sequencing technology. Soil Acidobacteria's alpha-diversity index and soil nutrient content differed significantly among different forest types. β-diversity and the composition of soil Acidobacteria also varied across forest types. Acidobacterial genera, such as Acidobacteria_Gp1, Acidobacteria_Gp4, and Acidobacteria_Gp17, play key roles in different forests. The RDA analyses pointed out that the soil pH, available nitrogen (AN), carbon to nitrogen (C/N) ratio, available phosphorus (AP), total carbon (TC), and total phosphorus (TP) were significant factors affecting soil Acidobacteria in different forest types. In this study, the diversity and composition of soil Acidobacteria under different forest types in a temperate forest ecosystem were analyzed, revealing the complex relationship between them and soil physicochemical properties. These findings not only enhance our understanding of soil microbial ecology but also provide important guidance for ecological conservation and restoration strategies for temperate forest ecosystems.
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Affiliation(s)
- Feng Jiao
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Lili Qian
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Jinhua Wu
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Dongdong Zhang
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Junying Zhang
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Mingyu Wang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Xin Sui
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Xianbang Zhang
- Heilongjiang Zhongyangzhan Black-Billed Capercaillie National Nature Reserve Service Center, Nenjiang 161400, China
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Andrade PHM, Machado PC, Paula AF, Paganin ACL, Rezende GS, Matheucci E, Carvalho LM, Freire CCM, Cunha AF, Lacava PT. 16S metabarcoding analysis reveals the influence of organic and conventional farming practices on bacterial communities from the rhizospheric of Coffea arabica L. BRAZ J BIOL 2023; 83:e274070. [PMID: 37937628 DOI: 10.1590/1519-6984.274070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 09/18/2023] [Indexed: 11/09/2023] Open
Abstract
Coffea sp. is cultivated in many tropical countries. Brazil has always adopted intensive agricultural practices, but organic coffee farming is an alternative system based on the non-use of agrochemicals and the rational management of soils. Metabarcoding 16S analysis using next-generation sequencing has been developed to identify and compare the diversity of the Coffea arabica L. rhizospheric bacterial community in two farming areas in São Paulo, Brazil. Dourado uses conventional farming, while Ribeirão Corrente uses organic. We found broad taxonomic composition, with sequences from 24 phyla, 55 classes, 61 orders, 146 families, and 337genus. The three most abundant phyla were Proteobacteria (38.27%), Actinobacteria (15.56%), and Acidobacteria (16.10%). In organic farming, the top 3 were the family Sphingomonadaceae, order Rhizobiales, genus Nocardioides, and Gp6. The genus Gp2 and the phylum Candidatus Saccharibacteria were the most abundant OTUs exclusively present in conventional farming. In the organic farming practice, Proteobacteria, Actinobacteria, and Acidobacteria were also present among the exclusive OTUs; we also found OTUs belonging to Bacteroidetes, Firmicutes, and Verrucomicrobia. Our study indicates a positive effect of organic farming on microbial communities. Fertilization may directly affect soil microbiota, suggesting that a large and active microbial community low in functional diversity might not adapt to new climatic conditions. A diverse community could provide better resilience to environmental changes, improving the productivity of this important crop.
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Affiliation(s)
- P H M Andrade
- Universidade Federal de São Carlos - UFSCar, Programa de Pós-graduação em Genética Evolutiva e Biologia Molecular, São Carlos, SP, Brasil
- Universidade Federal de São Carlos - UFSCar, Centro de Ciências Biológicas e da Saúde, Departamento de Morfologia e Patologia, Laboratório de Microbiologia e Biomoléculas, São Carlos, SP, Brasil
| | - P C Machado
- Universidade Federal de São Carlos - UFSCar, Centro de Ciências Biológicas e da Saúde, Departamento de Morfologia e Patologia, Laboratório de Microbiologia e Biomoléculas, São Carlos, SP, Brasil
- Universidade Federal de São Carlos - UFSCar, Programa de Pós-graduação em Biotecnologia, São Carlos, São Paulo, Brasil
| | - A F Paula
- Universidade Federal de São Carlos - UFSCar, Programa de Pós-graduação em Genética Evolutiva e Biologia Molecular, São Carlos, SP, Brasil
- Universidade Federal de São Carlos - UFSCar, Centro de Ciências Biológicas e da Saúde, Departamento de Morfologia e Patologia, Laboratório de Microbiologia e Biomoléculas, São Carlos, SP, Brasil
| | - A C L Paganin
- Universidade Federal de São Carlos - UFSCar, Departamento de Genética e Evolução, Laboratório de Bioquímica e Genética Aplicada, São Carlos, SP, Brasil
| | - G S Rezende
- Universidade Federal de São Carlos - UFSCar, Departamento de Genética e Evolução, Laboratório de Bioquímica e Genética Aplicada, São Carlos, SP, Brasil
| | - E Matheucci
- Universidade Federal de São Carlos - UFSCar, Programa de Pós-graduação em Biotecnologia, São Carlos, São Paulo, Brasil
- DNA Consult, São Carlos, SP, Brasil
| | - L M Carvalho
- Universidade Estadual de Campinas - Unicamp, Instituto de Biologia, Departamento de Genética e Evolução, Laboratório de Genômica e Expressão, Campinas, SP, Brasil
| | - C C M Freire
- Universidade Federal de São Carlos - UFSCar, Departamento de Genética e Evolução, Laboratório de Bioinformática Evolutiva, São Carlos, SP, Brasil
| | - A F Cunha
- Universidade Federal de São Carlos - UFSCar, Programa de Pós-graduação em Biotecnologia, São Carlos, São Paulo, Brasil
- Universidade Federal de São Carlos - UFSCar, Departamento de Genética e Evolução, Laboratório de Bioquímica e Genética Aplicada, São Carlos, SP, Brasil
| | - P T Lacava
- Universidade Federal de São Carlos - UFSCar, Centro de Ciências Biológicas e da Saúde, Departamento de Morfologia e Patologia, Laboratório de Microbiologia e Biomoléculas, São Carlos, SP, Brasil
- Universidade Federal de São Carlos - UFSCar, Programa de Pós-graduação em Biotecnologia, São Carlos, São Paulo, Brasil
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Li X, Meng Z, Chen K, Hu F, Liu L, Zhu T, Yang D. Comparing diversity patterns and processes of microbial community assembly in water column and sediment in Lake Wuchang, China. PeerJ 2023; 11:e14592. [PMID: 36627922 PMCID: PMC9826614 DOI: 10.7717/peerj.14592] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 11/28/2022] [Indexed: 01/06/2023] Open
Abstract
The study compare the diversity patterns and processes of microbial community assembly in the water and sediment of Lake Wuchang (China) using high-throughput sequencing of 16S rRNA gene amplicons. A higher microbial α-diversity in the sediment was revealed (P < 0.01), and the most common bacterial phyla in water column were Proteobacteria, Cyanobacteria and Actinobacteria, while Proteobacteria, Acidobacteria, Chloroflexi and Nitrospirae were dominant in sediment. Functions related to phototrophy and nitrogen metabolism primarily occurred in the water column and sediment, respectively. The microbial communities in water column from different seasons were divided into three groups, while no such dispersion in sediment based on PCoA and ANOSIM. According to Pearson correlation analysis, water temperature, dissolved oxygen, water depth, total nitrogen, ammonium, and nitrite were key factors in determining microbial community structure in water column, while TN in sediment, conductivity, and organic matter were key factors in sediment. However, the stochastic processes (|βNTI| < 2) dominated community assembly in both the water column and sediment of Lake Wuchang. These data will provide a foundation for microbial development and utilization in lake water column and sediment under the circumstances of increasing tendency of lake ecological fishery in China.
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de Souza LC, Procópio L. The adaptations of the microbial communities of the savanna soil over a period of wildfire, after the first rains, and during the rainy season. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:14070-14082. [PMID: 34601674 DOI: 10.1007/s11356-021-16731-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 09/22/2021] [Indexed: 06/13/2023]
Abstract
Annually, the Cerrado ecosystem alternates between dry periods and long rainy seasons. During the dry season, severe forest fires occur, consuming a considerable part of the native vegetation, which impacts directly on the microbiome of the soil. Evaluate the adaptations of the soil microbiome to drought, rain and wildfire. Sequencing of the 16S rRNA gene was carried out for three significant conditions: drought and forest fires ("Fire"), after the first recorded rains ("First_Rain"), and during the rainy season ("Rainy"). It has been shown that under the "Fire" condition, there was a predominance of Phylum Actinobacteria, followed by Proteobacteria and Firmicutes. With the advent of the rainy season, "First_Rain," there was a change in the predominant taxonomic groups, with a higher prevalence of members of Proteobacteria and Firmicutes. During the rainy season, Proteobacteria and Firmicutes continued as the most prevalent groups. However, it was noted that in this period, there was an increase in bacterial diversity when compared with other periods analyzed. These results show how environmental factors influence adaptations in microbial communities. This allows for a better understanding of how to link the structure of the microbial community to the performance of ecosystems, and assist in preventing the consequences of increased frequency of wildfires, and long periods of drought.
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Affiliation(s)
- Lucas Conceição de Souza
- Faculty of Geosciences (FAGEO), Universidade Federal do Mato Grosso (UFMT), Cuiabá, Mato Grosso, Brazil
| | - Luciano Procópio
- Industrial Microbiology and Bioremediation Department, Universidade Federal do Rio de Janeiro (UFRJ), Caxias, Rio de Janeiro, Brazil.
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Bobul'ská L, Espíndola SP, Coelho MA, Ferreira AS. Impact of land use on soil function and bacterial community in the Brazilian savanna. AN ACAD BRAS CIENC 2021; 93:e20201906. [PMID: 34550206 DOI: 10.1590/0001-3765202120201906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 03/20/2021] [Indexed: 11/21/2022] Open
Abstract
Land use systems have a great impact on soil function and microbial diversity in tropical soils. Our study aimed to evaluate soil biochemical indicators and community composition and to assess the relationship between soil biochemical and microbial indicators and bacterial diversity of three agroecosystems (pine forest, soya and sugarcane) and native Cerrado forest in the Brazilian savanna. Soil biochemical indicators (soil organic matter and enzymes) and high-throughput sequencing of 16S rDNA were performed in two topsoil depths (0-5 cm and 5-10 cm). Soil microbial and enzyme activity showed that agricultural soil usage has a negative impact on soil function compared to native and pine forests. Results also revealed higher enzyme activities in 0-5 cm depth compared to 5-10 cm depth, but enzymatic activities depend on land use systems. Soil bacterial community was affected by land use systems and depth, revealing changes in structure and abundance of bacterial composition. Alpha-diversity indexes were higher in the agricultural systems than in the forests, however they showed a significant negative correlation with most of the studied soil microbial and biochemical indicators. Our research had brought new relevant information about the relationship between the soil biochemical indicators and the bacterial diversity in the Brazilian Cerrado.
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Affiliation(s)
- Lenka Bobul'ská
- University of Prešov in Prešov, Department of Ecology, Faculty of Humanities and Natural Sciences, 17, November 1, Prešov 080 01, Slovakia
| | - Suéllen P Espíndola
- Universidade Federal de Uberlândia, Instituto de Ciências Agrárias, Campus Glória, Bloco CCG, 38410-337 Uberlândia, MG, Brazil
| | - Michelle A Coelho
- Universidade Federal de Uberlândia, Instituto de Ciências Agrárias, Campus Glória, Bloco CCG, 38410-337 Uberlândia, MG, Brazil
| | - Adão S Ferreira
- Universidade Federal de Uberlândia, Instituto de Ciências Agrárias, Campus Glória, Bloco CCG, 38410-337 Uberlândia, MG, Brazil
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7
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Xu R, Sun X, Häggblom MM, Dong Y, Zhang M, Yang Z, Xiao E, Xiao T, Gao P, Li B, Sun W. Metabolic potentials of members of the class Acidobacteriia in metal-contaminated soils revealed by metagenomic analysis. Environ Microbiol 2021; 24:803-818. [PMID: 34081382 DOI: 10.1111/1462-2920.15612] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 05/18/2021] [Accepted: 05/23/2021] [Indexed: 01/09/2023]
Abstract
The relative abundance of Acidobacteriia correlated positively with the concentrations of arsenic (As), mercury (Hg), chromium (Cr), copper (Cu) and other metals, suggesting their adaptation of the metal-rich environments. Metagenomic binning reconstructed 29 high-quality metagenome-assembled genomes (MAGs) associated with Acidobacteriia, providing an opportunity to study their metabolic potentials. These MAGs contained genes to transform As, Hg and Cr through oxidation, reduction, efflux and demethylation, suggesting the potential of Acidobacteriia to transform such metal(loid)s. Additionally, genes associated with alleviation of acidic and metal stress were also detected in these MAGs. Acidobacteriia may have the capabilities to resist or transform metal(loid)s in acidic metal-contaminated sites. Moreover, these genes encoding metal transformation could be also identified in the Acidobacteriia-associated MAGs from five additional metal-contaminated sites across Southwest China, as well as Acidobacteriia-associated reference genomes from the NCBI database, suggesting that the capability of metal transformation may be widespread among Acidobacteriia members. This discovery provides an understanding of metabolic potentials of the Acidobacteriia in acidic metal-rich sites.
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Affiliation(s)
- Rui Xu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China.,Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Xiaoxu Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China.,Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Max M Häggblom
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
| | - Yiran Dong
- School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, 430074, China
| | - Miaomiao Zhang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China.,Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Zhaohui Yang
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, China
| | - Enzong Xiao
- Key Laboratory of Water Quality and Conservation in the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Tangfu Xiao
- Key Laboratory of Water Quality and Conservation in the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Pin Gao
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China.,Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Baoqin Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China.,Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Weimin Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China.,Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China.,School of Environment, Henan Normal University, China.,Key Laboratory of Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, China
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Eskov AK, Zverev AO, Abakumov EV. Microbiomes in Suspended Soils of Vascular Epiphytes Differ from Terrestrial Soil Microbiomes and from Each Other. Microorganisms 2021; 9:microorganisms9051033. [PMID: 34064848 PMCID: PMC8150705 DOI: 10.3390/microorganisms9051033] [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: 03/28/2021] [Revised: 05/07/2021] [Accepted: 05/08/2021] [Indexed: 01/04/2023] Open
Abstract
Microbial biodiversity parameters for tropical rainforests remain poorly understood. Whilst the soil microbiome accounts up to 95% of the total diversity of microorganisms in terrestrial ecosystems, the microbiome of suspended soils formed by vascular epiphytes remains completely unexplored. Samples of ground and suspended soils were collected in Cat Tien National Park, southern Vietnam. DNA extraction and sequencing were performed, and libraries of 16s rDNA gene sequences were analyzed. Alpha diversity indices of the microorganisms were the highest in the forest ground soil. In general, the microbiological diversity of all the soil types was found to be similar at the phylum level. Taxonomic composition of the bacterial communities in the suspended soils of plants from the same species are not closer than the taxonomic compositions of the communities in the suspended soils of different plant species. However, the beta diversity analysis revealed significant differences in the movement of mineral elements in terrestrial versus suspended soils. Our data showed that the suspended soils associated with vascular epiphytes were a depository of unique microbiological biodiversity. A contributing factor was the presence of large amounts of organic matter in the suspended soils-deposits collected by the epiphytes-which would have been degraded by termites if it had reached the ground. Further, the nutrient content of the suspended soils was prime for soil respiration activity and taxonomic microbial community biodiversity.
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Affiliation(s)
- Alen K. Eskov
- Faculty of Biology, Lomonosov Moscow State University, 1–12 Leninskie Gory, 119991 Moscow, Russia
- Tzitzin Main Botanical Garden, Russian Academy of Sciences, 4 Botanicheskaya ul., 117628 Moscow, Russia
- Correspondence:
| | - Alexei O. Zverev
- Faculty of Biology, Saint-Petersburg State University, 7/9 Universitetskaya nab., 199034 St. Petersburg, Russia; (A.O.Z.); (E.V.A.)
- All-Russian Research Institute for Agricultural Microbiology, 3 Podbelsky chausse, 196608 St. Petersburg, Russia
| | - Evgeny V. Abakumov
- Faculty of Biology, Saint-Petersburg State University, 7/9 Universitetskaya nab., 199034 St. Petersburg, Russia; (A.O.Z.); (E.V.A.)
- All-Russian Research Institute for Agricultural Microbiology, 3 Podbelsky chausse, 196608 St. Petersburg, Russia
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9
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Distribution patterns of Acidobacteriota in different fynbos soils. PLoS One 2021; 16:e0248913. [PMID: 33750980 PMCID: PMC7984625 DOI: 10.1371/journal.pone.0248913] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 03/09/2021] [Indexed: 11/28/2022] Open
Abstract
The Acidobacteriota is ubiquitous and is considered as one of the major bacterial phyla in soils. The current taxonomic classifications of this phylum are divided into 15 class-level subdivisions (SDs), with only 5 of these SDs containing cultured and fully described species. Within the fynbos biome, the Acidobacteriota has been reported as one of the dominant bacterial phyla, with relative abundances ranging between 4–26%. However, none of these studies reported on the specific distribution and diversity of the Acidobacteriota within these soils. Therefore, in this study we aimed to first determine the relative abundance and diversity of the Acidobacteriota in three pristine fynbos nature reserve soils, and secondly, whether differences in the acidobacterial composition can be attributed to environmental factors, such as soil abiotic properties. A total of 27 soil samples were collected at three nature reserves, namely Jonkershoek, Hottentots Holland, and Kogelberg. The variable V4-V5 region of the 16S rRNA gene was sequenced using the Ion Torrent S5 platform. The mean relative abundance of the Acidobacteriota were 9.02% for Jonkershoek, 14.91% for Kogelberg, and most significantly (p<0.05), 18.42% for Hottentots Holland. A total of 33 acidobacterial operational taxonomic units (OTUs) were identified. The dominant subdivisions identified in all samples included SDs 1, 2, and 3. Significant differences were observed in the distribution and composition of these OTUs between nature reserves. The SD1 were negatively correlated to soil pH, hydrogen (H+), potassium (K+) and carbon (C). In contrast, SD2, was positively correlated to soil pH, phosphorus (P), and K+, and unclassified members of SD3 was positively correlated to H+, K, and C. This study is the first to report on the specific acidobacterial distribution in pristine fynbos soils in South Africa.
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Dom SP, Ikenaga M, Lau SYL, Radu S, Midot F, Yap ML, Chin MY, Lo ML, Jee MS, Maie N, Melling L. Linking prokaryotic community composition to carbon biogeochemical cycling across a tropical peat dome in Sarawak, Malaysia. Sci Rep 2021; 11:6416. [PMID: 33742002 PMCID: PMC7979770 DOI: 10.1038/s41598-021-81865-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 01/11/2021] [Indexed: 01/31/2023] Open
Abstract
Tropical peat swamp forest is a global store of carbon in a water-saturated, anoxic and acidic environment. This ecosystem holds diverse prokaryotic communities that play a major role in nutrient cycling. A study was conducted in which a total of 24 peat soil samples were collected in three forest types in a tropical peat dome in Sarawak, Malaysia namely, Mixed Peat Swamp (MPS), Alan Batu (ABt), and Alan Bunga (ABg) forests to profile the soil prokaryotic communities through meta 16S amplicon analysis using Illumina Miseq. Results showed these ecosystems were dominated by anaerobes and fermenters such as Acidobacteria, Proteobacteria, Actinobacteria and Firmicutes that cover 80-90% of the total prokaryotic abundance. Overall, the microbial community composition was different amongst forest types and depths. Additionally, this study highlighted the prokaryotic communities' composition in MPS was driven by higher humification level and lower pH whereas in ABt and ABg, the less acidic condition and higher organic matter content were the main factors. It was also observed that prokaryotic diversity and abundance were higher in the more oligotrophic ABt and ABg forest despite the constantly waterlogged condition. In MPS, the methanotroph Methylovirgula ligni was found to be the major species in this forest type that utilize methane (CH4), which could potentially be the contributing factor to the low CH4 gas emissions. Aquitalea magnusonii and Paraburkholderia oxyphila, which can degrade aromatic compounds, were the major species in ABt and ABg forests respectively. This information can be advantageous for future study in understanding the underlying mechanisms of environmental-driven alterations in soil microbial communities and its potential implications on biogeochemical processes in relation to peatland management.
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Affiliation(s)
- Simon Peter Dom
- Sarawak Tropical Peat Research Institute, Lot 6035, Kuching-Samarahan Expressway, 94300, Kota Samarahan, Sarawak, Malaysia
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Makoto Ikenaga
- Research Field in Agriculture, Agriculture Fisheries and Veterinary Medicine Area, Kagoshima University, 1-21-24, Korimoto, Kagoshima, 890-0065, Japan
| | - Sharon Yu Ling Lau
- Sarawak Tropical Peat Research Institute, Lot 6035, Kuching-Samarahan Expressway, 94300, Kota Samarahan, Sarawak, Malaysia.
| | - Son Radu
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Frazer Midot
- Sarawak Tropical Peat Research Institute, Lot 6035, Kuching-Samarahan Expressway, 94300, Kota Samarahan, Sarawak, Malaysia
| | - Mui Lan Yap
- Sarawak Tropical Peat Research Institute, Lot 6035, Kuching-Samarahan Expressway, 94300, Kota Samarahan, Sarawak, Malaysia
| | - Mei-Yee Chin
- Sarawak Tropical Peat Research Institute, Lot 6035, Kuching-Samarahan Expressway, 94300, Kota Samarahan, Sarawak, Malaysia
| | - Mei Lieng Lo
- Sarawak Tropical Peat Research Institute, Lot 6035, Kuching-Samarahan Expressway, 94300, Kota Samarahan, Sarawak, Malaysia
| | - Mui Sie Jee
- Sarawak Tropical Peat Research Institute, Lot 6035, Kuching-Samarahan Expressway, 94300, Kota Samarahan, Sarawak, Malaysia
| | - Nagamitsu Maie
- School of Veterinary Medicine, Kitasato University, Towada, Aomori, 034-8628, Japan
| | - Lulie Melling
- Sarawak Tropical Peat Research Institute, Lot 6035, Kuching-Samarahan Expressway, 94300, Kota Samarahan, Sarawak, Malaysia
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11
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Seasonal and Agricultural Response of Acidobacteria Present in Two Fynbos Rhizosphere Soils. DIVERSITY-BASEL 2020. [DOI: 10.3390/d12070277] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The Acidobacteria is one of the most abundant phyla in most soil types. Fynbos plants are endemic to South Africa, and these soils provide the ideal habitat for Acidobacteria, because of its low pH and oligotrophic properties. However, little is known about their distribution in the fynbos biome and the impact of cultivation of plants on Acidobacterial diversity. Therefore, the aim of this study was to determine the effect of seasonal changes and cultivation on the relative abundance and diversity of Acidobacteria associated with Aspalathus linearis (rooibos) and Cyclopia spp. (honeybush). This study was based on rhizosphere soil. A total of 32 and 31 operational taxonomic units (OTUs) were identified for honeybush and rooibos, respectively. The majority of these were classified as representatives of subdivisions 1, 2, 3, and 10. Significant differences in community compositions were observed between seasons for both honeybush and rooibos, as well as between the cultivated and uncultivated honeybush. Acidobacteria had a significantly positive correlation with pH, C, Ca2+, and P. In this study, we have shown the effect of seasonal changes, in summer and winter, and cultivation farming on the relative abundance and diversity of Acidobacteria present in the soil of rooibos and honeybush.
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Trentini CP, Campanello PI, Villagra M, Ferreras J, Hartmann M. Thinning Partially Mitigates the Impact of Atlantic Forest Replacement by Pine Monocultures on the Soil Microbiome. Front Microbiol 2020; 11:1491. [PMID: 32719665 PMCID: PMC7350009 DOI: 10.3389/fmicb.2020.01491] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 06/08/2020] [Indexed: 11/28/2022] Open
Abstract
Forest replacement by exotic plantations drive important changes at the level of the overstory, understory and forest floor. In the Atlantic Forest of northern Argentina, large areas have been replaced by loblolly pine (Pinus taeda L.) monocultures. Plant and litter transformation, together with harvesting operations, change microclimatic conditions and edaphic properties. Management practices such as thinning promote the development of native understory vegetation and could counterbalance negative effects of forest replacement on soil. Here, the effects of pine plantations and thinning on physical, chemical and microbiological soil properties were assessed. Bacterial, archaeal, and fungal community structure were analyzed using a metabarcoding approach targeting ribosomal markers. Forest replacement and, to a lesser extent, thinning practices in the pine plantations induced significant changes in soil physico-chemical properties and associated shifts in bacterial and fungal communities. Most measured physical and chemical properties were altered due to forest replacement, but a few of these properties reached values similar to natural forests under the thinning operation. Fungal alpha diversity decreased in pine plantations, whereas bacterial alpha diversity tended to increase but with little statistical support. Shifts in community composition were observed for both fungal and bacterial domains, and were mostly related to changes in plant understory composition, soil carbon, organic matter, water content, pH and bulk density. Among several other changes, highly abundant phyla such as Proteobacteria (driven by many genera) and Mortierellomycota (mainly driven by Mortierella) decreased in relative abundance in the plantations, whereas Acidobacteria (mainly driven by Acidothermus and Candidatus Koribacter) and Basidiomycota (mainly driven by the ectomycorrhiza Russula) showed the opposite response. Taken together, these results provide insights into the effects of forest replacement on belowground properties and elucidate the potentially beneficial effect of thinning practices in intensive plantation systems through promoting the understory development. Although thinning did not entirely counterbalance the effects of forest replacement on physical, chemical and biological soil properties, the strategy helped mitigating the effects and might promote resilience of these properties by the end of the rotation cycle, if subsequent management practices compatible with the development of a native understory vegetation are applied.
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Affiliation(s)
- Carolina Paola Trentini
- Laboratorio de Ecología Forestal y Ecofisiología, Instituto de Biología Subtropical, CONICET-UNaM, Puerto Iguazú, Misiones, Argentina
| | - Paula Inés Campanello
- Centro de Estudios Ambientales Integrados, Facultad de Ingeniería, Universidad Nacional de la Patagonia San Juan Bosco, CONICET, Esquel, Argentina
| | - Mariana Villagra
- Laboratorio de Ecología Forestal y Ecofisiología, Instituto de Biología Subtropical, CONICET-UNaM, Puerto Iguazú, Misiones, Argentina
| | - Julian Ferreras
- Grupo de Investigación en Genética Aplicada, Instituto de Biología Subtropical, CONICET-UNaM, Posadas, Misiones, Argentina
| | - Martin Hartmann
- Sustainable Agroecosystems, Department of Environmental Systems Science, Institute of Agricultural Sciences, ETH Zürich, Zurich, Switzerland
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13
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Chernov TI, Zhelezova AD, Tkhakakhova AK, Bgazhba NA, Zverev AO. Microbiomes of Virgin Soils of Southern Vietnam Tropical Forests. Microbiology (Reading) 2019. [DOI: 10.1134/s0026261719040040] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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14
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de Chaves MG, Silva GGZ, Rossetto R, Edwards RA, Tsai SM, Navarrete AA. Acidobacteria Subgroups and Their Metabolic Potential for Carbon Degradation in Sugarcane Soil Amended With Vinasse and Nitrogen Fertilizers. Front Microbiol 2019; 10:1680. [PMID: 31417506 PMCID: PMC6682628 DOI: 10.3389/fmicb.2019.01680] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 07/08/2019] [Indexed: 11/21/2022] Open
Abstract
Acidobacteria is a predominant bacterial phylum in tropical agricultural soils, including sugarcane cultivated soils. The increased need for fertilizers due to the expansion of sugarcane production is a threat to the ability of the soil to maintain its potential for self-regulation in the long term, in witch carbon degradation has essential role. In this study, a culture-independent approach based on high-throughput DNA sequencing and microarray technology was used to perform taxonomic and functional profiling of the Acidobacteria community in a tropical soil under sugarcane (Saccharum spp.) that was supplemented with nitrogen (N) combined with vinasse. These analyses were conducted to identify the subgroup-level responses to chemical changes and the carbon (C) degradation potential of the different Acidobacteria subgroups. Eighteen Acidobacteria subgroups from a total of 26 phylogenetically distinct subgroups were detected based on high-throughput DNA sequencing, and 16 gene families associated with C degradation were quantified using Acidobacteria-derived DNA microarray probes. The subgroups Gp13 and Gp18 presented the most positive correlations with the gene families associated with C degradation, especially those involved in hemicellulose degradation. However, both subgroups presented low abundance in the treatment containing vinasse. In turn, the Gp4 subgroup was the most abundant in the treatment that received vinasse, but did not present positive correlations with the gene families for C degradation analyzed in this study. The metabolic potential for C degradation of the different Acidobacteria subgroups in sugarcane soil amended with N and vinasse can be driven in part through the increase in soil nutrient availability, especially calcium (Ca), magnesium (Mg), potassium (K), aluminum (Al), boron (B) and zinc (Zn). This soil management practice reduces the abundance of Acidobacteria subgroups, including those potentially involved with C degradation in this agricultural soil.
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Affiliation(s)
- Miriam Gonçalves de Chaves
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
| | | | - Raffaella Rossetto
- São Paulo's Agency for Agribusiness Technology APTA-SAA, Piracicaba, Brazil
| | - Robert Alan Edwards
- Computational Science Research Center, San Diego State University, San Diego, CA, United States
| | - Siu Mui Tsai
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Acacio Aparecido Navarrete
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil.,Department of Environmental Sciences, Federal University of São Carlos, Sorocaba, Brazil
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15
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D'Auria G, Artacho A, Rojas RA, Bautista JS, Méndez R, Gamboa MT, Gamboa JR, Gómez-Cruz R. Metagenomics of Bacterial Diversity in Villa Luz Caves with Sulfur Water Springs. Genes (Basel) 2018; 9:E55. [PMID: 29361802 PMCID: PMC5793206 DOI: 10.3390/genes9010055] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 01/12/2018] [Accepted: 01/13/2018] [Indexed: 01/22/2023] Open
Abstract
New biotechnology applications require in-depth preliminary studies of biodiversity. The methods of massive sequencing using metagenomics and bioinformatics tools offer us sufficient and reliable knowledge to understand environmental diversity, to know new microorganisms, and to take advantage of their functional genes. Villa Luz caves, in the southern Mexican state of Tabasco, are fed by at least 26 groundwater inlets, containing 300-500 mg L-1 H2S and <0.1 mg L-1 O2. We extracted environmental DNA for metagenomic analysis of collected samples in five selected Villa Luz caves sites, with pH values from 2.5 to 7. Foreign organisms found in this underground ecosystem can oxidize H2S to H2SO4. These include: biovermiculites, a bacterial association that can grow on the rock walls; snottites, that are whitish, viscous biofilms hanging from the rock walls, and sacks or bags of phlegm, which live within the aquatic environment of the springs. Through the emergency food assistance program (TEFAP) pyrosequencing, a total of 20,901 readings of amplification products from hypervariable regions V1 and V3 of 16S rRNA bacterial gene in whole and pure metagenomic DNA samples were generated. Seven bacterial phyla were identified. As a result, Proteobacteria was more frequent than Acidobacteria. Finally, acidophilic Proteobacteria was detected in UJAT5 sample.
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Affiliation(s)
- Giuseppe D'Auria
- Sequencing and Bioinformatics Service, Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO), Valencia 46020.
| | - Alejandro Artacho
- Center for Advanced Research in Public Health, Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO), Valencia 46020.
| | - Rafael A Rojas
- Chemical Engineering Faculty, Exact Sciences and Engineering Campus, Autonomous University of Yucatán (UADY), Mérida, Yucatán 97050..
| | - José S Bautista
- Biological Sciences Academic Division, Autonomous University Juárez de Tabasco (UJAT), Villahermosa, Centro, Tabasco 99630, Mexico.
| | - Roberto Méndez
- Biological Sciences Academic Division, Autonomous University Juárez de Tabasco (UJAT), Villahermosa, Centro, Tabasco 99630, Mexico.
| | - María T Gamboa
- Biological Sciences Academic Division, Autonomous University Juárez de Tabasco (UJAT), Villahermosa, Centro, Tabasco 99630, Mexico.
| | - Jesús R Gamboa
- Biological Sciences Academic Division, Autonomous University Juárez de Tabasco (UJAT), Villahermosa, Centro, Tabasco 99630, Mexico.
| | - Rodolfo Gómez-Cruz
- Biological Sciences Academic Division, Autonomous University Juárez de Tabasco (UJAT), Villahermosa, Centro, Tabasco 99630, Mexico.
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16
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Wegner CE, Liesack W. Unexpected Dominance of Elusive Acidobacteria in Early Industrial Soft Coal Slags. Front Microbiol 2017; 8:1023. [PMID: 28642744 PMCID: PMC5462947 DOI: 10.3389/fmicb.2017.01023] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 05/22/2017] [Indexed: 11/19/2022] Open
Abstract
Acid mine drainage (AMD) and mine tailing environments are well-characterized ecosystems known to be dominated by organisms involved in iron- and sulfur-cycling. Here we examined the microbiology of industrial soft coal slags that originate from alum leaching, an ecosystem distantly related to AMD environments. Our study involved geochemical analyses, bacterial community profiling, and shotgun metagenomics. The slags still contained high amounts of alum constituents (aluminum, sulfur), which mediated direct and indirect effects on bacterial community structure. Bacterial groups typically found in AMD systems and mine tailings were not present. Instead, the soft coal slags were dominated by uncharacterized groups of Acidobacteria (DA052 [subdivision 2], KF-JG30-18 [subdivision 13]), Actinobacteria (TM214), Alphaproteobacteria (DA111), and Chloroflexi (JG37-AG-4), which have previously been detected primarily in peatlands and uranium waste piles. Shotgun metagenomics allowed us to reconstruct 13 high-quality Acidobacteria draft genomes, of which two genomes could be directly linked to dominating groups (DA052, KF-JG30-18) by recovered 16S rRNA gene sequences. Comparative genomics revealed broad carbon utilization capabilities for these two groups of elusive Acidobacteria, including polysaccharide breakdown (cellulose, xylan) and the competence to metabolize C1 compounds (ribulose monophosphate pathway) and lignin derivatives (dye-decolorizing peroxidases). Equipped with a broad range of efflux systems for metal cations and xenobiotics, DA052 and KF-JG30-18 may have a competitive advantage over other bacterial groups in this unique habitat.
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Affiliation(s)
- Carl-Eric Wegner
- Department of Biogeochemistry, Max Planck Institute for Terrestrial MicrobiologyMarburg, Germany
- Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University JenaJena, Germany
| | - Werner Liesack
- Department of Biogeochemistry, Max Planck Institute for Terrestrial MicrobiologyMarburg, Germany
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17
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Mineral Types and Tree Species Determine the Functional and Taxonomic Structures of Forest Soil Bacterial Communities. Appl Environ Microbiol 2017; 83:AEM.02684-16. [PMID: 28003192 DOI: 10.1128/aem.02684-16] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 12/15/2016] [Indexed: 11/20/2022] Open
Abstract
Although minerals represent important soil constituents, their impact on the diversity and structure of soil microbial communities remains poorly documented. In this study, pure mineral particles with various chemistries (i.e., obsidian, apatite, and calcite) were considered. Each mineral type was conditioned in mesh bags and incubated in soil below different tree stands (beech, coppice with standards, and Corsican pine) for 2.5 years to determine the relative impacts of mineralogy and mineral weatherability on the taxonomic and functional diversities of mineral-associated bacterial communities. After this incubation period, the minerals and the surrounding bulk soil were collected to determine mass loss and to perform soil analyses, enzymatic assays, and cultivation-dependent and -independent analyses. Notably, our 16S rRNA gene pyrosequencing analyses revealed that after the 2.5-year incubation period, the mineral-associated bacterial communities strongly differed from those of the surrounding bulk soil for all tree stands considered. When focusing only on minerals, our analyses showed that the bacterial communities associated with calcite, the less recalcitrant mineral type, significantly differed from those that colonized obsidian and apatite minerals. The cultivation-dependent analysis revealed significantly higher abundances of effective mineral-weathering bacteria on the most recalcitrant minerals (i.e., apatite and obsidian). Together, our data showed an enrichment of Betaproteobacteria and effective mineral-weathering bacteria related to the Burkholderia and Collimonas genera on the minerals, suggesting a key role for these taxa in mineral weathering and nutrient cycling in nutrient-poor forest ecosystems.IMPORTANCE Forests are usually developed on nutrient-poor and rocky soils, while nutrient-rich soils have been dedicated to agriculture. In this context, nutrient recycling and nutrient access are key processes in such environments. Deciphering how soil mineralogy influences the diversity, structure, and function of soil bacterial communities in relation to the soil conditions is crucial to better understanding the relative role of the soil bacterial communities in nutrient cycling and plant nutrition in nutrient-poor environments. The present study determined in detail the diversity and structure of bacterial communities associated with different mineral types incubated for 2.5 years in the soil under different tree species using cultivation-dependent and -independent analyses. Our data showed an enrichment of specific bacterial taxa on the minerals, specifically on the most weathered minerals, suggesting that they play key roles in mineral weathering and nutrient cycling in nutrient-poor forest ecosystems.
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18
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Val-Moraes SP, de Macedo HS, Kishi LT, Pereira RM, Navarrete AA, Mendes LW, de Figueiredo EB, La Scala N, Tsai SM, de Macedo Lemos EG, Alves LMC. Liming in the sugarcane burnt system and the green harvest practice affect soil bacterial community in northeastern São Paulo, Brazil. Antonie van Leeuwenhoek 2016; 109:1643-1654. [PMID: 27629424 DOI: 10.1007/s10482-016-0764-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 08/31/2016] [Indexed: 01/12/2023]
Abstract
Here we show that both liming the burnt sugarcane and the green harvest practice alter bacterial community structure, diversity and composition in sugarcane fields in northeastern São Paulo state, Brazil. Terminal restriction fragment length polymorphism fingerprinting and 16S rRNA gene cloning and sequencing were used to analyze changes in soil bacterial communities. The field experiment consisted of sugarcane-cultivated soils under different regimes: green sugarcane (GS), burnt sugarcane (BS), BS in soil amended with lime applied to increase soil pH (BSL), and native forest (NF) as control soil. The bacterial community structures revealed disparate patterns in sugarcane-cultivated soils and forest soil (R = 0.786, P = 0.002), and overlapping patterns were shown for the bacterial community structure among the different management regimes applied to sugarcane (R = 0.194, P = 0.002). The numbers of operational taxonomic units (OTUs) found in the libraries were 117, 185, 173 and 166 for NF, BS, BSL and GS, respectively. Sugarcane-cultivated soils revealed higher bacterial diversity than NF soil, with BS soil accounting for a higher richness of unique OTUs (101 unique OTUs) than NF soil (23 unique OTUs). Cluster analysis based on OTUs revealed similar bacterial communities in NF and GS soils, while the bacterial community from BS soil was most distinct from the others. Acidobacteria and Alphaproteobacteria were the most abundant bacterial phyla across the different soils with Acidobacteria Gp1 accounting for a higher abundance in NF and GS soils than burnt sugarcane-cultivated soils (BS and BSL). In turn, Acidobacteria Gp4 abundance was higher in BS soils than in other soils. These differential responses in soil bacterial community structure, diversity and composition can be associated with the agricultural management, mainly liming practices, and harvest methods in the sugarcane-cultivated soils, and they can be detected shortly after harvest.
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Affiliation(s)
- Silvana Pompeia Val-Moraes
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinária FCAV, Univ. Estadual Paulista UNESP, Acesso Prof. Dr. Paulo Donato Castellane, S/N, Jaboticabal, SP, 14884-900, Brazil.
| | - Helena Suleiman de Macedo
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinária FCAV, Univ. Estadual Paulista UNESP, Acesso Prof. Dr. Paulo Donato Castellane, S/N, Jaboticabal, SP, 14884-900, Brazil
| | - Luciano Takeshi Kishi
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinária FCAV, Univ. Estadual Paulista UNESP, Acesso Prof. Dr. Paulo Donato Castellane, S/N, Jaboticabal, SP, 14884-900, Brazil
| | - Rodrigo Matheus Pereira
- Faculdade de Ciências Biológicas e Ambientais FCBA, Universidade Federal da Grande Dourados UFGD, Rodovia Dourados, Itahum, Km 12 - Unidade II, Caixa Postal: 364, Dourados, MS, CEP 79804-970, Brazil
| | - Acacio Aparecido Navarrete
- Laboratório de Biologia Celular e Molecular, Centro de Energia Nuclear na Agricultura CENA, Universidade de São Paulo USP, Av. Centenário, 303, Caixa Postal 96, Piracicaba, SP, CEP 13400-970, Brazil
| | - Lucas William Mendes
- Laboratório de Biologia Celular e Molecular, Centro de Energia Nuclear na Agricultura CENA, Universidade de São Paulo USP, Av. Centenário, 303, Caixa Postal 96, Piracicaba, SP, CEP 13400-970, Brazil
| | - Eduardo Barretto de Figueiredo
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinária FCAV, Univ. Estadual Paulista UNESP, Acesso Prof. Dr. Paulo Donato Castellane, S/N, Jaboticabal, SP, 14884-900, Brazil
| | - Newton La Scala
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinária FCAV, Univ. Estadual Paulista UNESP, Acesso Prof. Dr. Paulo Donato Castellane, S/N, Jaboticabal, SP, 14884-900, Brazil
| | - Siu Mui Tsai
- Laboratório de Biologia Celular e Molecular, Centro de Energia Nuclear na Agricultura CENA, Universidade de São Paulo USP, Av. Centenário, 303, Caixa Postal 96, Piracicaba, SP, CEP 13400-970, Brazil
| | - Eliana Gertrudes de Macedo Lemos
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinária FCAV, Univ. Estadual Paulista UNESP, Acesso Prof. Dr. Paulo Donato Castellane, S/N, Jaboticabal, SP, 14884-900, Brazil
| | - Lúcia Maria Carareto Alves
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinária FCAV, Univ. Estadual Paulista UNESP, Acesso Prof. Dr. Paulo Donato Castellane, S/N, Jaboticabal, SP, 14884-900, Brazil.
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Nunes I, Jacquiod S, Brejnrod A, Holm PE, Johansen A, Brandt KK, Priemé A, Sørensen SJ. Coping with copper: legacy effect of copper on potential activity of soil bacteria following a century of exposure. FEMS Microbiol Ecol 2016; 92:fiw175. [DOI: 10.1093/femsec/fiw175] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/16/2016] [Indexed: 12/18/2022] Open
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20
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Kielak AM, Barreto CC, Kowalchuk GA, van Veen JA, Kuramae EE. The Ecology of Acidobacteria: Moving beyond Genes and Genomes. Front Microbiol 2016; 7:744. [PMID: 27303369 PMCID: PMC4885859 DOI: 10.3389/fmicb.2016.00744] [Citation(s) in RCA: 454] [Impact Index Per Article: 56.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 05/03/2016] [Indexed: 12/01/2022] Open
Abstract
The phylum Acidobacteria is one of the most widespread and abundant on the planet, yet remarkably our knowledge of the role of these diverse organisms in the functioning of terrestrial ecosystems remains surprisingly rudimentary. This blatant knowledge gap stems to a large degree from the difficulties associated with the cultivation of these bacteria by classical means. Given the phylogenetic breadth of the Acidobacteria, which is similar to the metabolically diverse Proteobacteria, it is clear that detailed and functional descriptions of acidobacterial assemblages are necessary. Fortunately, recent advances are providing a glimpse into the ecology of members of the phylum Acidobacteria. These include novel cultivation and enrichment strategies, genomic characterization and analyses of metagenomic DNA from environmental samples. Here, we couple the data from these complementary approaches for a better understanding of their role in the environment, thereby providing some initial insights into the ecology of this important phylum. All cultured acidobacterial type species are heterotrophic, and members of subdivisions 1, 3, and 4 appear to be more versatile in carbohydrate utilization. Genomic and metagenomic data predict a number of ecologically relevant capabilities for some acidobacteria, including the ability to: use of nitrite as N source, respond to soil macro-, micro nutrients and soil acidity, express multiple active transporters, degrade gellan gum and produce exopolysaccharide (EPS). Although these predicted properties allude to a competitive life style in soil, only very few of these prediction shave been confirmed via physiological studies. The increased availability of genomic and physiological information, coupled to distribution data in field surveys and experiments, should direct future progress in unraveling the ecology of this important but still enigmatic phylum.
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Affiliation(s)
- Anna M Kielak
- Department of Microbial Ecology, The Netherlands Institute of Ecology - Koninklijke Nederlandse Akademie van Wetenschappen Wageningen, Netherlands
| | - Cristine C Barreto
- Graduate Program in Genomic Sciences and Biotechnology, Universidade Católica de Brasília Brasília, Brazil
| | - George A Kowalchuk
- Ecology and Biodiversity Group, University of Utrecht Utrecht, Netherlands
| | - Johannes A van Veen
- Department of Microbial Ecology, The Netherlands Institute of Ecology - Koninklijke Nederlandse Akademie van Wetenschappen Wageningen, Netherlands
| | - Eiko E Kuramae
- Department of Microbial Ecology, The Netherlands Institute of Ecology - Koninklijke Nederlandse Akademie van Wetenschappen Wageningen, Netherlands
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Souza RC, Mendes IC, Reis-Junior FB, Carvalho FM, Nogueira MA, Vasconcelos ATR, Vicente VA, Hungria M. Shifts in taxonomic and functional microbial diversity with agriculture: How fragile is the Brazilian Cerrado? BMC Microbiol 2016; 16:42. [PMID: 26983403 PMCID: PMC4794851 DOI: 10.1186/s12866-016-0657-z] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 03/02/2016] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The Cerrado--an edaphic type of savannah--comprises the second largest biome of the Brazilian territory and is the main area for grain production in the country, but information about the impact of land conversion to agriculture on microbial diversity is still scarce. We used a shotgun metagenomic approach to compare undisturbed (native) soil and soils cropped for 23 years with soybean/maize under conservation tillage--"no-till" (NT)--and conventional tillage (CT) systems in the Cerrado biome. RESULTS Soil management and fertilizer inputs with the introduction of agriculture improved chemical properties, but decreased soil macroporosity and microbial biomass of carbon and nitrogen. Principal coordinates analyses confirmed different taxonomic and functional profiles for each treatment. There was predominance of the Bacteria domain, especially the phylum Proteobacteria, with higher numbers of sequences in the NT and CT treatments; Archaea and Viruses also had lower numbers of sequences in the undisturbed soil. Within the Alphaproteobacteria, there was dominance of Rhizobiales and of the genus Bradyrhizobium in the NT and CT systems, attributed to massive inoculation of soybean, and also of Burkholderiales. In contrast, Rhizobium, Azospirillum, Xanthomonas, Pseudomonas and Acidobacterium predominated in the native Cerrado. More Eukaryota, especially of the phylum Ascomycota were detected in the NT. The functional analysis revealed lower numbers of sequences in the five dominant categories for the CT system, whereas the undisturbed Cerrado presented higher abundance. CONCLUSION High impact of agriculture in taxonomic and functional microbial diversity in the biome Cerrado was confirmed. Functional diversity was not necessarily associated with taxonomic diversity, as the less conservationist treatment (CT) presented increased taxonomic sequences and reduced functional profiles, indicating a strategy to try to maintain soil functioning by favoring taxa that are probably not the most efficient for some functions. Our results highlight that underneath the rustic appearance of the Cerrado vegetation there is a fragile soil microbial community.
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Affiliation(s)
- Renata Carolini Souza
- />Embrapa Soja, Soil Biotechnology, C.P. 231, 86001-970 Londrina, PR Brazil
- />Department Microbiology, Universidade Federal do Paraná, C.P. 19031, 81531-990 Curitiba, PR Brazil
| | - Iêda Carvalho Mendes
- />Embrapa Cerrado, Soil Microbiology, C.P. 08223, 73301-970 Planaltina, DF Brazil
| | | | | | | | | | - Vânia Aparecida Vicente
- />Department Microbiology, Universidade Federal do Paraná, C.P. 19031, 81531-990 Curitiba, PR Brazil
| | - Mariangela Hungria
- />Embrapa Soja, Soil Biotechnology, C.P. 231, 86001-970 Londrina, PR Brazil
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22
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Navarrete AA, Venturini AM, Meyer KM, Klein AM, Tiedje JM, Bohannan BJM, Nüsslein K, Tsai SM, Rodrigues JLM. Differential Response of Acidobacteria Subgroups to Forest-to-Pasture Conversion and Their Biogeographic Patterns in the Western Brazilian Amazon. Front Microbiol 2015; 6:1443. [PMID: 26733981 PMCID: PMC4686610 DOI: 10.3389/fmicb.2015.01443] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 12/03/2015] [Indexed: 11/13/2022] Open
Abstract
Members of the phylum Acidobacteria are among the most abundant soil bacteria on Earth, but little is known about their response to environmental changes. We asked how the relative abundance and biogeographic patterning of this phylum and its subgroups responded to forest-to-pasture conversion in soils of the western Brazilian Amazon. Pyrosequencing of 16S rRNA genes was employed to assess the abundance and composition of the Acidobacteria community across 54 soil samples taken using a spatially nested sampling scheme at the landscape level. Numerically, Acidobacteria represented 20% of the total bacterial community in forest soils and 11% in pasture soils. Overall, 15 different Acidobacteria subgroups of the current 26 subgroups were detected, with Acidobacteria subgroups 1, 3, 5, and 6 accounting together for 87% of the total Acidobacteria community in forest soils and 75% in pasture soils. Concomitant with changes in soil chemistry after forest-to-pasture conversion—particularly an increase in properties linked to soil acidity and nutrient availability—we observed an increase in the relative abundances of Acidobacteria subgroups 4, 10, 17, and 18, and a decrease in the relative abundances of other Acidobacteria subgroups in pasture relative to forest soils. The composition of the total Acidobacteria community as well as the most abundant Acidobacteria subgroups (1, 3, 5, and 6) was significantly more similar in composition across space in pasture soils than in forest soils. These results suggest that preponderant responses of Acidobacteria subgroups, especially subgroups 1, 3, 4, 5, and 6, to forest-to-pasture conversion effects in soils could be used to define management-indicators of agricultural practices in the Amazon Basin. These acidobacterial responses are at least in part through alterations on acidity- and nutrient-related properties of the Amazon soils.
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Affiliation(s)
- Acacio A Navarrete
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo Piracicaba, Brazil
| | - Andressa M Venturini
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo Piracicaba, Brazil
| | - Kyle M Meyer
- Department of Biology, Institute of Ecology and Evolution, University of Oregon Eugene, OR, USA
| | - Ann M Klein
- Department of Biology, Institute of Ecology and Evolution, University of Oregon Eugene, OR, USA
| | - James M Tiedje
- Department of Plant, Soil and Microbial Sciences, Center for Microbial Ecology, Michigan State University East Lansing, MI, USA
| | - Brendan J M Bohannan
- Department of Biology, Institute of Ecology and Evolution, University of Oregon Eugene, OR, USA
| | - Klaus Nüsslein
- Department of Microbiology, University of Massachusetts Amherst, MA, USA
| | - Siu M Tsai
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo Piracicaba, Brazil
| | - Jorge L M Rodrigues
- Department of Land, Air and Water Resources, University of California, Davis Davis, CA, USA
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23
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Esposito A, Ahmed E, Ciccazzo S, Sikorski J, Overmann J, Holmström SJM, Brusetti L. Comparison of Rock Varnish Bacterial Communities with Surrounding Non-Varnished Rock Surfaces: Taxon-Specific Analysis and Morphological Description. MICROBIAL ECOLOGY 2015; 70:741-750. [PMID: 25921518 DOI: 10.1007/s00248-015-0617-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 04/16/2015] [Indexed: 06/04/2023]
Abstract
Rock varnish is a thin layer of Fe and Mn oxyhydroxides with embedded clay minerals that contain an increased Mn/Fe ratio compared to that of the Earth's crust. Even if the study of rock varnish has important implications in several fields, the composition of epilithic bacterial communities and the distribution of taxa on varnish surfaces are still not wholly described. The aim of this study was (i) to identify the bacterial taxa which show the greatest variation between varnish and non-varnish environments, collected from the same rock, and (ii) to describe the morphology of epilithic communities through scanning electron microscopy (SEM). Triplicate samples of rock surfaces with varnish and triplicate samples without varnish were collected from five sites in Matsch Valley (South Tyrol, Italy). The V4 region of 16S rRNA gene was analyzed by Illumina sequencing. Fifty-five ubiquitous taxa have been examined to assess variation between varnish and non-varnish. Cyanobacteria, Chloroflexi, Proteobacteria along with minor taxa such as Solirubrobacterales, Conexibaxter, and Rhodopila showed significant variations of abundance, diversity, or both responding to the ecology (presence/absence of varnish). Other taxa, such as the genus Edaphobacter, showed a more marked spatial variation responding to the sampling site. SEM images showed a multitude of bacterial morphologies and structures involved in the process of attachment and creation of a suitable environment for growth. The features emerging from this analysis suggest that the highly oxidative Fe and Mn-rich varnish environment favors anoxigenic autotrophy and establishment of highly specialized bacteria.
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Affiliation(s)
- Alfonso Esposito
- Faculty of Science and Technology, Free University of Bozen-Bolzano, Piazza Università 1, I-39100, Bozen-Bolzano, Italy
| | - Engy Ahmed
- Department of Geological Sciences, Stockholm University, SE-10691, Stockholm, Sweden
| | - Sonia Ciccazzo
- Faculty of Science and Technology, Free University of Bozen-Bolzano, Piazza Università 1, I-39100, Bozen-Bolzano, Italy
| | - Johannes Sikorski
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7 B, D-38124, Braunschweig, Germany
| | - Jörg Overmann
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7 B, D-38124, Braunschweig, Germany
| | - Sara J M Holmström
- Department of Geological Sciences, Stockholm University, SE-10691, Stockholm, Sweden
| | - Lorenzo Brusetti
- Faculty of Science and Technology, Free University of Bozen-Bolzano, Piazza Università 1, I-39100, Bozen-Bolzano, Italy.
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24
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Emerson KJ, Conn JE, Bergo ES, Randel MA, Sallum MAM. Brazilian Anopheles darlingi Root (Diptera: Culicidae) Clusters by Major Biogeographical Region. PLoS One 2015; 10:e0130773. [PMID: 26172559 PMCID: PMC4501553 DOI: 10.1371/journal.pone.0130773] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 05/23/2015] [Indexed: 11/18/2022] Open
Abstract
The major drivers of the extensive biodiversity of the Neotropics are proposed to be geological and tectonic events together with Pliocene and Pleistocene environmental and climatic change. Geographical barriers represented by the rivers Amazonas/Solimões, the Andes and the coastal mountain ranges in eastern Brazil have been hypothesized to lead to diversification within the primary malaria vector, Anopheles (Nyssorhynchus) darlingi Root, which primarily inhabits rainforest. To test this biogeographical hypothesis, we analyzed 786 single nucleotide polymorphisms (SNPs) in 12 populations of An. darlingi from across the complex Brazilian landscape. Both model-based (STRUCTURE) and non-model-based (Principal Components and Discriminant Analysis) analysis of population structure detected three major genetic clusters that correspond with newly described Neotropical biogeographical regions: 1) Atlantic Forest province (= southeast population); 2) Parana Forest province (= West Atlantic forest population, with one Chacoan population - SP); and 3) Brazilian dominion population (= Amazonian population with one Chacoan population - TO). Significant levels of pairwise genetic divergences were found among the three clusters, allele sharing among clusters was negligible, and geographical distance did not contribute to differentiation. We infer that the Atlantic forest coastal mountain range limited dispersal between the Atlantic Forest province and the Parana Forest province populations, and that the large, diagonal open vegetation region of the Chacoan dominion dramatically reduced dispersal between the Parana and Brazilian dominion populations. We hypothesize that the three genetic clusters may represent three putative species.
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Affiliation(s)
- Kevin J. Emerson
- Biology Department, St. Mary’s College of Maryland, St. Mary’s City, Maryland, United States of America
| | - Jan E. Conn
- The Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
- Department of Biomedical Sciences—School of Public Health, SUNY Albany, Albany, New York, United States of America
| | - Eduardo S. Bergo
- Superintendência de Controle de Endemias, Secretaria de Estado da Saúde de São Paulo, Araraquara, São Paulo, Brazil
| | - Melissa A. Randel
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Maria Anice M. Sallum
- Departamento de Epidemiologia, Faculdade de Saúde Pública, Universidade de São Paulo, São Paulo, Brazil
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