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Prekrasna I, Pavlovska M, Miryuta N, Dzhulai A, Dykyi E, Convey P, Kozeretska I, Bedernichek T, Parnikoza I. Antarctic Hairgrass Rhizosphere Microbiomes: Microscale Effects Shape Diversity, Structure, and Function. Microbes Environ 2022; 37. [PMID: 35705309 PMCID: PMC9530728 DOI: 10.1264/jsme2.me21069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The rhizosphere microbiome of the native Antarctic hairgrass Deschampsia antarctica from the central maritime Antarctic was investigated using 16S RNA metagenomics and compared to those of the second native Antarctic plant Colobanthus quitensis and closely related temperate D. cespitosa. The rhizosphere microbial communities of D. antarctica and D. cespitosa had high taxon richness, while that of C. quitensis had markedly lower diversity. The majority of bacteria in the rhizosphere communities of the hairgrass were affiliated to Proteobacteria, Bacteroidetes, and Actinobacteria. The rhizosphere of C. quitensis was dominated by Actinobacteria. All microbial communities included high proportions of unique amplicon sequence variants (ASVs) and there was high heterogeneity between samples at the ASV level. The soil parameters examined did not explain this heterogeneity. Bacteria belonging to Actinobacteria, Bacteroidetes, and Proteobacteria were sensitive to fluctuations in the soil surface temperature. The values of the United Soil Surface Temperature Influence Index (UTII, Iti) showed that variations in most microbial communities from Galindez Island were associated with microscale variations in temperature. Metabolic predictions in silico using PICRUSt 2.0, based on the taxonomically affiliated part of the microbiomes, showed similarities with the rhizosphere community of D. antarctica in terms of the predicted functional repertoire. The results obtained indicate that these communities are involved in the primary processes of soil development (particularly the degradation of lignin and lignin-derived compounds) in the central maritime Antarctic and may be beneficial for the growth of Antarctic vascular plants. However, due to the limitations associated with interpreting PICRUSt 2.0 outputs, these predictions need to be verified experimentally.
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Affiliation(s)
| | - Mariia Pavlovska
- State Institution National Antarctic Scientific Center.,National University of Life and Environmental Sciences of Ukraine
| | | | - Artem Dzhulai
- State Institution National Antarctic Scientific Center
| | - Evgen Dykyi
- State Institution National Antarctic Scientific Center
| | - Peter Convey
- British Antarctic Survey, NERC.,Department of Zoology, University of Johannesburg
| | | | | | - Ivan Parnikoza
- State Institution National Antarctic Scientific Center.,Institute of Molecular Biology and Genetics.,National University of "Kyiv-Mohyla Academy"
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Wang R, Wang M, Wang J, Lin Y. Habitats Are More Important Than Seasons in Shaping Soil Bacterial Communities on the Qinghai-Tibetan Plateau. Microorganisms 2021; 9:microorganisms9081595. [PMID: 34442674 PMCID: PMC8400953 DOI: 10.3390/microorganisms9081595] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/19/2021] [Accepted: 07/23/2021] [Indexed: 11/16/2022] Open
Abstract
Both habitats and seasons can determine the dynamics of microbial communities, but the relative importance of different habitats and seasonal changes in shaping the soil bacterial community structures on a small spatial scale in permafrost areas remains controversial. In this study, we explored the relative effect of four typical alpine meadow habitats (swamp wetland, swamp meadow, meadow and mature meadow) versus seasons on soil bacterial communities based on samples from the Qinghai-Tibetan Plateau in four months (March, May, July and September). The results showed that habitats, rather than seasons explained more variation of soil bacterial composition and structure. Environmental cofactors explained the greatest proportion of bacterial variation observed and can help elucidate the driving force of seasonal changes and habitats on bacterial communities. Soil temperature played the most important role in shaping bacterial beta diversities, followed by soil total nitrogen and pH. A group of microbial biomarkers, used as indicators of different months, were identified using random forest modeling, and for which relative abundance was shaped by different environmental factors. Furthermore, seasonality in bacterial co-occurrence patterns was observed. The data showed that co-occurrence relationships changed over months. The inter-taxa connections in May and July were more pronounced than that in March and September. Bryobacter, a genus of subgroup_22 affiliated to Acidobacteria, and Pseudonocardia belonging to Actinobacteria were observed as the keystone taxa in different months in the network. These results demonstrate that the bacterial community was clustered according to the seasonal mechanism, whereas the co-occurrence relationships changed over months, which indicated complex bacterial dynamics in a permafrost grassland on the eastern edge of Qinghai-Tibetan.
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Affiliation(s)
- Rui Wang
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing 100091, China; (R.W.); (J.W.)
| | - Miao Wang
- Party School of the Chengdu Committee of the Chinese Communist Party, Chengdu 610110, China;
| | - Jing Wang
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing 100091, China; (R.W.); (J.W.)
| | - Yinghua Lin
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing 100091, China; (R.W.); (J.W.)
- Correspondence: ; Tel.: +86-13671160455
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Cao Y, Yu X, Ju F, Zhan H, Jiang B, Kang H, Xie Z. Airborne bacterial community diversity, source and function along the Antarctic Coast. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 765:142700. [PMID: 33069481 DOI: 10.1016/j.scitotenv.2020.142700] [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: 07/18/2020] [Revised: 09/11/2020] [Accepted: 09/26/2020] [Indexed: 06/11/2023]
Abstract
Antarctica is an isolated and relatively simple ecosystem dominated by microorganisms, providing a rare opportunity to study the spread of airborne microbes and to predict future global climate change. However, little is known about on the diversity and potential sources of microorganisms in the marine atmosphere along the Antarctica coast. Here we explored the airborne bacterial community (i.e., bacteriome) diversity, sources and functional potential along the Antarctic coast based on 16S rRNA gene amplicon sequencing of 25 bioaerosol samples collected during the 33rd Xuelong Antarctic scientific expedition. The results showed that bacterial communities in the Antarctic bioaerosols i) were predominated by Proteobacteria (91.3%) including Sphingomonas, ii) showed relative low alpha-diversity but high spatiotemporal variabilities; and iii) were potentially immigrated with terrestrial, marine and Antarctic polar bacteria through long-range transport and sea-air exchange pathways. Moreover, canonical correspondence analysis of bacteriome composition showed that wind speed, temperature, and organic carbon had a significant effect on the bacterial community (P < 0.05), although bacterial richness (Richness index) and diversity (Simpson index and Shannon index) showed no statistically significant differences between rainy, cloudy and snowy weather conditions (Adjust P > 0.05, ANOVA, Tukey HSD test). iv) The functional profiles predicted by Tax4fun2 suggest high representation of function genes related to fatty acid biosynthesis and metabolism, amino acid metabolism, nucleotide metabolism, and carbohydrate metabolism, which is conducive to the formation of microlayers on the surface of the ocean and the survival and growth of bacteria.
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Affiliation(s)
- Yue Cao
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Xiawei Yu
- Anhui Key Laboratory of Polar Environment and Global Change & Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Feng Ju
- School of Engineering, Westlake University, Hangzhou 310024, China; Key Laboratory of Coastal Environment and Resource Research of Zhejiang Province, School of Engineering, Westlake University, Hangzhou 310024, China
| | - Haicong Zhan
- Anhui Key Laboratory of Polar Environment and Global Change & Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Bei Jiang
- Anhui Key Laboratory of Polar Environment and Global Change & Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Hui Kang
- Anhui Key Laboratory of Polar Environment and Global Change & Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Zhouqing Xie
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China; Anhui Key Laboratory of Polar Environment and Global Change & Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, China; Center for Excellence in Urban Atmospheric Environment, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, Fujian 361021, China.
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Hemmat-Jou MH, Safari-Sinegani AA, Che R, Mirzaie-Asl A, Tahmourespour A, Tahmasbian I. Toxic trace element resistance genes and systems identified using the shotgun metagenomics approach in an Iranian mine soil. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:4845-4856. [PMID: 32949366 DOI: 10.1007/s11356-020-10824-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 09/13/2020] [Indexed: 05/27/2023]
Abstract
This study aimed to identify the microbial communities, resistance genes, and resistance systems in an Iranian mine soil polluted with toxic trace elements (TTE). The polluted soil samples were collected from a mining area and compared against non-polluted (control) collected soils from the vicinity of the mine. The soil total DNA was extracted and sequenced, and bioinformatic analysis of the assembled metagenomes was conducted to identify soil microbial biodiversity, TTE resistance genes, and resistance systems. The results of the employed shotgun approach indicated that the relative abundance of Proteobacteria, Firmicutes, Bacteroidetes, and Deinococcus-Thermus was significantly higher in the TTE-polluted soils compared with those in the control soils, while the relative abundance of Actinobacteria and Acidobacteria was significantly lower in the polluted soils. The high concentration of TTE increased the ratio of archaea to bacteria and decreased the alpha diversity in the polluted soils compared with the control soils. Canonical correspondence analysis (CCA) demonstrated that heavy metal pollution was the major driving factor in shaping microbial communities compared with any other soil characteristics. In the identified heavy metal resistome (HV-resistome) of TTE-polluted soils, major functional pathways were carbohydrates metabolism, stress response, amino acid and derivative metabolism, clustering-based subsystems, iron acquisition and metabolism, cell wall synthesis and capsulation, and membrane transportation. Ten TTE resistance systems were identified in the HV-resistome of TTE-polluted soils, dominated by "P-type ATPases," "cation diffusion facilitators," and "heavy metal efflux-resistance nodulation cell division (HME-RND)." Most of the resistance genes (69%) involved in resistance systems are affiliated to cell wall, outer membrane, periplasm, and cytoplasmic membrane. The finding of this study provides insight into the microbial community in Iranian TTE-polluted soils and their resistance genes and systems.
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Affiliation(s)
| | | | - Rongxiao Che
- Institute of International Rivers and Eco-security, Yunnan University, Kunming, 650091, China
| | - Asghar Mirzaie-Asl
- Department of Biotechnology, Bu-Ali Sina University, Hamedan, 6517838695, Iran
| | - Arezoo Tahmourespour
- Department of Basic Medical Sciences, Islamic Azad University (Isfahan Branch), Isfahan, Iran
| | - Iman Tahmasbian
- Department of Agriculture and Fisheries, Queensland Government, Toowoomba, QLD, 4350, Australia
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Malcheva B, Nustorova M, Zhiyanski M, Sokolovska M, Yaneva R, Abakumov E. Diversity and activity of microorganisms in Antarctic polar soils. ONE ECOSYSTEM 2020. [DOI: 10.3897/oneeco.5.e51816] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The study is focused on microbiological analyses in polar soils in selected monitoring sites in Livingstone Island, Antarctica region. The analyses include determination of the quantity and qualitative composition of the heterotrophic block of soil microflora (non-spore-forming bacteria, bacilli, actinomycetes, micromycetes, bacteria absorbing mineral nitrogen), insofar as it plays a major role in the element cycling and soil formation processes. Aerobic (rapidly and slowly growing) and anaerobic groups of soil microorganisms were investigated and the biogenicity (total microflora) and the rate of mineralisation processes (mineralisation coefficient) were determined. Mostly non-spore-forming aerobic bacteria, followed by actinomycetes, are dominant in determining the biogenicity of the studied polar soils. The rearrangement of the microorganisms in the composition of the total microflora by degree of dominance indicates the participation of all the studied groups of microorganisms in most sites in the initial and final stages of the decomposition of organic matter. The mineralisation of soils is most active in sites with vegetation cover. The established pigmentation in aerobic microorganisms is probably due to their good adaptation and protection under extreme polar conditions, while the absence of oxygen impedes the formation of pigments.
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Gadkari PS, McGuinness LR, Männistö MK, Kerkhof LJ, Häggblom MM. Arctic tundra soil bacterial communities active at subzero temperatures detected by stable isotope probing. FEMS Microbiol Ecol 2019; 96:5645228. [DOI: 10.1093/femsec/fiz192] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 11/26/2019] [Indexed: 12/14/2022] Open
Abstract
ABSTRACT
Arctic soils store vast amounts of carbon and are subject to intense climate change. While the effects of thaw on the composition and activities of Arctic tundra microorganisms has been examined extensively, little is known about the consequences of temperature fluctuations within the subzero range in seasonally frozen or permafrost soils. This study identified tundra soil bacteria active at subzero temperatures using stable isotope probing (SIP). Soils from Kilpisjärvi, Finland, were amended with 13C-cellobiose and incubated at 0, −4 and −16°C for up to 40 weeks. 16S rRNA gene sequence analysis of 13C-labelled DNA revealed distinct subzero-active bacterial taxa. The SIP experiments demonstrated that diverse bacteria, including members of Candidatus Saccharibacteria, Melioribacteraceae, Verrucomicrobiaceae, Burkholderiaceae, Acetobacteraceae, Armatimonadaceae and Planctomycetaceae, were capable of synthesising 13C-DNA at subzero temperatures. Differences in subzero temperature optima were observed, for example, with members of Oxalobacteraceae and Rhizobiaceae found to be more active at 0°C than at −4°C or −16°C, whereas Melioribacteriaceae were active at all subzero temperatures tested. Phylogeny of 13C-labelled 16S rRNA genes from the Melioribacteriaceae, Verrucomicrobiaceae and Candidatus Saccharibacteria suggested that these taxa formed subzero-active clusters closely related to members from other cryo-environments. This study demonstrates that subzero temperatures impact active bacterial community composition and activity, which may influence biogeochemical cycles.
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Affiliation(s)
- Preshita S Gadkari
- School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick NJ 08901, USA
| | - Lora R McGuinness
- Department of Marine and Coastal Sciences, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Minna K Männistö
- Natural Resources Institute Finland, P.O. Box 16, FI-96301 Rovaniemi, Finland
| | - Lee J Kerkhof
- Department of Marine and Coastal Sciences, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Max M Häggblom
- School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick NJ 08901, USA
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7
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Newsham KK, Tripathi BM, Dong K, Yamamoto N, Adams JM, Hopkins DW. Bacterial Community Composition and Diversity Respond to Nutrient Amendment but Not Warming in a Maritime Antarctic Soil. MICROBIAL ECOLOGY 2019; 78:974-984. [PMID: 30989354 DOI: 10.1007/s00248-019-01373-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 03/22/2019] [Indexed: 06/09/2023]
Abstract
A resumption of climate warming in maritime Antarctica, arising from continued greenhouse gas emissions to the atmosphere, is predicted to lead to further expansions of plant populations across the region, with consequent increases in nutrient inputs to soils. Here, we test the main and interactive effects of warming, applied with open top chambers (OTCs), and nutrient amendment with tryptic soy broth (TSB), an artificial growth substrate, on bacterial community composition and diversity using Illumina sequencing of 16S rRNA genes in soil from a field experiment in the southern maritime Antarctic. Substantial effects of TSB application on bacterial communities were identified after 49 months, including reduced diversity, altered phylogenetic community assembly processes, increased Proteobacteria-to-Acidobacteria ratios and significant divergence in community composition, notably increases in the relative abundances of the gram-positive genera Arthrobacter, Paeniglutamicibacter and Planococcus. Contrary to previous observations from other maritime Antarctic field warming experiments, we recorded no effects of warming with OTCs, or interactive effects of OTCs and TSB application, on bacterial community composition or diversity. Based on these findings, we conclude that further warming of the maritime Antarctic is unlikely to influence soil bacterial community composition or diversity directly, but that increased nutrient inputs arising from enhanced plant growth across the region may affect the composition of soil bacterial communities, with possible effects on ecosystem productivity.
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Affiliation(s)
- Kevin K Newsham
- NERC British Antarctic Survey, Madingley Road, Cambridge, CB3 0ET, UK.
| | - Binu M Tripathi
- Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Ke Dong
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Gyeonggi-do, 16227, Republic of Korea
| | - Naomichi Yamamoto
- Department of Environmental Health Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Jonathan M Adams
- Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - David W Hopkins
- Scotland's Rural College, Peter Wilson Building, West Mains Road, Edinburgh, EH9 3JG, UK
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8
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Chrismas NAM, Williamson CJ, Yallop ML, Anesio AM, Sánchez-Baracaldo P. Photoecology of the Antarctic cyanobacterium Leptolyngbya sp. BC1307 brought to light through community analysis, comparative genomics and in vitro photophysiology. Mol Ecol 2019; 27:5279-5293. [PMID: 30565777 DOI: 10.1111/mec.14953] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 10/11/2018] [Indexed: 12/17/2022]
Abstract
Cyanobacteria are important photoautotrophs in extreme environments such as the McMurdo Dry Valleys, Antarctica. Terrestrial Antarctic cyanobacteria experience constant darkness during the winter and constant light during the summer which influences the ability of these organisms to fix carbon over the course of an annual cycle. Here, we present a unique approach combining community structure, genomic and photophysiological analyses to understand adaptation to Antarctic light regimes in the cyanobacterium Leptolyngbya sp. BC1307. We show that Leptolyngbya sp. BC1307 belongs to a clade of cyanobacteria that inhabits near-surface environments in the McMurdo Dry Valleys. Genomic analyses reveal that, unlike close relatives, Leptolyngbya sp. BC1307 lacks the genes necessary for production of the pigment phycoerythrin and is incapable of complimentary chromatic acclimation, while containing several genes responsible for known photoprotective pigments. Photophysiology experiments confirmed Leptolyngbya sp. BC1307 to be tolerant of short-term exposure to high levels of photosynthetically active radiation, while sustained exposure reduced its capacity for photoprotection. As such, Leptolyngbya sp. BC1307 likely exploits low-light microenvironments within cyanobacterial mats in the McMurdo Dry Valleys.
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Affiliation(s)
- Nathan A M Chrismas
- Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth, UK.,School of Geographical Sciences, University of Bristol, Bristol, UK
| | - Christopher J Williamson
- School of Geographical Sciences, University of Bristol, Bristol, UK.,School of Biological Sciences, Life Sciences Building, University of Bristol, Bristol, UK
| | - Marian L Yallop
- School of Biological Sciences, Life Sciences Building, University of Bristol, Bristol, UK
| | - Alexandre M Anesio
- School of Geographical Sciences, University of Bristol, Bristol, UK.,Department of Environmental Sciences, Aarhus University, Roskilde, Denmark
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Soil bacterial diversity is positively associated with air temperature in the maritime Antarctic. Sci Rep 2019; 9:2686. [PMID: 30804443 PMCID: PMC6389919 DOI: 10.1038/s41598-019-39521-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 01/25/2019] [Indexed: 02/01/2023] Open
Abstract
Terrestrial ecosystems in the maritime Antarctic experienced rapid warming during the latter half of the 20th century. While warming ceased at the turn of the millennium, significant increases in air temperature are expected later this century, with predicted positive effects on soil fungal diversity, plant growth and ecosystem productivity. Here, by sequencing 16S ribosomal RNA genes in 40 soils sampled from along a 1,650 km climatic gradient through the maritime Antarctic, we determine whether rising air temperatures might similarly influence the diversity of soil bacteria. Of 22 environmental factors, mean annual surface air temperature was the strongest and most consistent predictor of soil bacterial diversity. Significant, but weaker, associations between bacterial diversity and soil moisture content, C:N ratio, and Ca, Mg, PO43− and dissolved organic C concentrations were also detected. These findings indicate that further rises in air temperature in the maritime Antarctic may enhance terrestrial ecosystem productivity through positive effects on soil bacterial diversity.
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10
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Lambrechts S, Willems A, Tahon G. Uncovering the Uncultivated Majority in Antarctic Soils: Toward a Synergistic Approach. Front Microbiol 2019; 10:242. [PMID: 30828325 PMCID: PMC6385771 DOI: 10.3389/fmicb.2019.00242] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 01/29/2019] [Indexed: 01/22/2023] Open
Abstract
Although Antarctica was once believed to be a sterile environment, it is now clear that the microbial communities inhabiting the Antarctic continent are surprisingly diverse. Until the beginning of the new millennium, little was known about the most abundant inhabitants of the continent: prokaryotes. From then on, however, the rising use of deep sequencing techniques has led to a better understanding of the Antarctic prokaryote diversity and provided insights in the composition of prokaryotic communities in different Antarctic environments. Although these cultivation-independent approaches can produce millions of sequences, linking these data to organisms is hindered by several problems. The largest difficulty is the lack of biological information on large parts of the microbial tree of life, arising from the fact that most microbial diversity on Earth has never been characterized in laboratory cultures. These unknown prokaryotes, also known as microbial dark matter, have been dominantly detected in all major environments on our planet. Laboratory cultures provide access to the complete genome and the means to experimentally verify genomic predictions and metabolic functions and to provide evidence of horizontal gene transfer. Without such well-documented reference data, microbial dark matter will remain a major blind spot in deep sequencing studies. Here, we review our current understanding of prokaryotic communities in Antarctic ice-free soils based on cultivation-dependent and cultivation-independent approaches. We discuss advantages and disadvantages of both approaches and how these strategies may be combined synergistically to strengthen each other and allow a more profound understanding of prokaryotic life on the frozen continent.
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Affiliation(s)
- Sam Lambrechts
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | | | - Guillaume Tahon
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
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11
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Hemmat-Jou MH, Safari-Sinegani AA, Mirzaie-Asl A, Tahmourespour A. Analysis of microbial communities in heavy metals-contaminated soils using the metagenomic approach. ECOTOXICOLOGY (LONDON, ENGLAND) 2018; 27:1281-1291. [PMID: 30242595 DOI: 10.1007/s10646-018-1981-x] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 09/01/2018] [Indexed: 06/08/2023]
Abstract
Soil pollution occurring at mining sites has adverse impacts on soil microbial diversity. New approaches, such as metagenomics approach, have become a powerful tool to investigate biodiversity of soil microbial communities. In the current study, metagenomics approach was used to investigate the microbial diversity of soils contaminated with different concentrations of lead (Pb) and zinc (Zn). The contaminated soils were collected from a Pb and Zn mine. The soil total DNA was extracted and 16S rDNA genes were amplified using universal primers. The PCR amplicons were sequenced and bioinformatic analysis of metagenomes was conducted to identify prokaryotic diversity in the Pb- and Zn-contaminated soils. The results indicated that the ten most abundant bacteria in all samples were Solirubrobacter (Actinobacteria), Geobacter (Proteobacteria), Edaphobacter (Acidobacteria), Pseudomonas (Proteobacteria), Gemmatiomonas (Gemmatimonadetes), Nitrosomonas, Xanthobacter, and Sphingomonas (Proteobacteria), Pedobacter (Bacterioidetes), and Ktedonobacter (Chloroflexi), descendingly. Archaea were also numerous, and Nitrososphaerales which are important in the nitrogen cycle had the highest abundance in the samples. Although, alpha and beta diversity showed negative effects of Pb and Zn contamination on soil microbial communities, microbial diversity of the contaminated soils was not subjected to a significant change. This study provided valuable insights into microbial composition in heavy metals-contaminated soils.
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Affiliation(s)
- M H Hemmat-Jou
- Department of Soil Science, College of Agriculture, Bu-Ali Sina University, Hamedan, 6517838695, Iran.
| | - A A Safari-Sinegani
- Department of Soil Science, College of Agriculture, Bu-Ali Sina University, Hamedan, 6517838695, Iran
| | - A Mirzaie-Asl
- Department of Biotechnology, College of Agriculture, Bu-Ali Sina University, Hamedan, 6517838695, Iran
| | - A Tahmourespour
- Department of Basic Medical Sciences, Isfahan (Khorasgan) Branch, Islamic Azad University, Isfahan, Iran
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Tahon G, Tytgat B, Lebbe L, Carlier A, Willems A. Abditibacterium utsteinense sp. nov., the first cultivated member of candidate phylum FBP, isolated from ice-free Antarctic soil samples. Syst Appl Microbiol 2018; 41:279-290. [DOI: 10.1016/j.syapm.2018.01.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 01/20/2018] [Accepted: 01/29/2018] [Indexed: 10/18/2022]
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13
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Bacteria from Antarctic environments: diversity and detection of antimicrobial, antiproliferative, and antiparasitic activities. Polar Biol 2018. [DOI: 10.1007/s00300-018-2300-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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14
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Baeza M, Barahona S, Alcaíno J, Cifuentes V. Amplicon-Metagenomic Analysis of Fungi from Antarctic Terrestrial Habitats. Front Microbiol 2017; 8:2235. [PMID: 29184546 PMCID: PMC5694453 DOI: 10.3389/fmicb.2017.02235] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 10/31/2017] [Indexed: 01/08/2023] Open
Abstract
In cold environments such as polar regions, microorganisms play important ecological roles, and most of our knowledge about them comes from studies of cultivable microorganisms. Metagenomic technologies are powerful tools that can give a more comprehensive assessment of microbial communities, and the amplification of rDNA followed by next-generation sequencing has given good results in studies aimed particularly at environmental microorganisms. Culture-independent studies of microbiota in terrestrial habitats of Antarctica, which is considered the driest, coldest climate on Earth, are increasing and indicate that micro-diversity is much higher than previously thought. In this work, the microbial diversity of terrestrial habitats including eight islands of the South Shetland Archipelago, two islands on the Antarctic Peninsula and Union Glacier, was studied by amplicon-metagenome analysis. Molecular analysis of the studied localities clustered together the islands of the South Shetland Archipelago, except Greenwich Island, and separated them from the Litchfield and Lagotellerie islands and Union Glacier, which is in agreement with the latitudinal difference among them. Among fungi, 87 genera and 123 species were found, of which species belonging to 37 fungal genera not previously cultivated from Antarctica were detected. Phylogenetic analysis, including the closest BLAST-hit sequences, clustered fungi in 11 classes being the most represented Lecanoromycetes and Eurotiomycetes.
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Affiliation(s)
- Marcelo Baeza
- Laboratorio de Genética, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
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Avoidance of protein oxidation correlates with the desiccation and radiation resistance of hot and cold desert strains of the cyanobacterium Chroococcidiopsis. Extremophiles 2017; 21:981-991. [DOI: 10.1007/s00792-017-0957-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 08/21/2017] [Indexed: 12/29/2022]
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16
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Pulschen AA, Bendia AG, Fricker AD, Pellizari VH, Galante D, Rodrigues F. Isolation of Uncultured Bacteria from Antarctica Using Long Incubation Periods and Low Nutritional Media. Front Microbiol 2017; 8:1346. [PMID: 28769908 PMCID: PMC5509766 DOI: 10.3389/fmicb.2017.01346] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Accepted: 07/03/2017] [Indexed: 12/16/2022] Open
Abstract
Uncultured microorganisms comprise most of the microbial diversity existing on our planet. Despite advances in environmental sequencing and single-cell genomics, in-depth studies about bacterial metabolism and screening of novel bioproducts can only be assessed by culturing microbes in the laboratory. Here we report uncultured, or recalcitrant, microorganisms from an Antarctic soil sample, using relatively simple methods: oligotrophic media, extended incubation periods, observation under stereo microscopy, and selection of slow-growing bacteria. We managed to isolate several rare microorganisms belonging to infrequently isolated or recently described genera, for example Lapillicoccus, Flavitalea, Quadrisphaera, Motilibacter, and Polymorphobacter. Additionally, we obtained isolates presenting 16S rRNA sequence similarity ranging from 92.08 to 94.46% with any other known cultured species, including two distinct isolates from the class Thermoleophilia, that although common in Antarctic soils (as identified by metagenomics), was never reported to be isolated from such samples. Our data indicates that simple methods are still useful for cultivating recalcitrant microorganisms, even when dealing with samples from extreme environments.
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Affiliation(s)
| | - Amanda G Bendia
- Departamento de Oceanografia Biológica, Instituto Oceanográfico, Universidade de São PauloButantã, Brazil
| | | | - Vivian H Pellizari
- Departamento de Oceanografia Biológica, Instituto Oceanográfico, Universidade de São PauloButantã, Brazil
| | - Douglas Galante
- Laboratório Nacional de Luz Síncrotron, Centro Nacional de Pesquisa em Energia e MateriaisCampinas, Brazil
| | - Fabio Rodrigues
- Departamento de Química Fundamental, Instituto de Química, Universidade de São PauloButantã, Brazil
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17
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Rigonato J, Gama WA, Alvarenga DO, Branco LHZ, Brandini FP, Genuário DB, Fiore MF. Aliterella atlantica gen. nov., sp. nov., and Aliterella antarctica sp. nov., novel members of coccoid Cyanobacteria. Int J Syst Evol Microbiol 2016; 66:2853-2861. [PMID: 27054834 DOI: 10.1099/ijsem.0.001066] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Two Cyanobacteria isolated from South Atlantic Ocean continental shelf deep water and from a marine green algae inhabiting the Admiralty Bay, King George Island, Antarctica were investigated based on morphological and ultrastructural traits, phylogeny of 16S rRNA gene sequences, secondary structure of the 16S-23S internal transcribed spacer regions and phylogenomic analyses. The majority of these evaluations demonstrated that both strains differ from the genera of cyanobacteria with validly published names and, therefore, supported the description of the novel genus as Aliterella gen. nov. The identity and phylogeny of 16S rRNA gene sequences, together with the secondary structure of D1D1' and BoxB intergenic regions, further supported the two strains representing distinct species: Aliterella atlantica gen. nov., sp. nov. (type SP469036, strain CENA595T) and Aliterella antarctica sp. nov. (type SP469035, strain CENA408T). The phylogenomic analysis of A. atlantica sp. nov. CENA595T, based on 21 protein sequences, revealed that this genus belongs to the cyanobacterial order Chroococcidiopsidales. The isolation and cultivation of two geographically distant unicellular members of a novel cyanobacterial genus and the sequenced genome of the type strain bring new insights into the current classification of the coccoid group, and into the reconstruction of their evolutionary history.
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Affiliation(s)
- Janaina Rigonato
- University of São Paulo, Center for Nuclear Energy in Agriculture, Avenida Centenário 303, 13400-970 Piracicaba, SP, Brazil
| | - Watson Arantes Gama
- Institute of Botany, Nucleus of Phycology, Avenida Miguel Estéfano 3687, 04301-012 São Paulo, SP, Brazil
| | - Danillo Oliveira Alvarenga
- University of São Paulo, Center for Nuclear Energy in Agriculture, Avenida Centenário 303, 13400-970 Piracicaba, SP, Brazil
| | - Luis Henrique Zanini Branco
- São Paulo State University UNESP, Institute of Bioscience, Languages and Exact Sciences, São José do Rio Preto, São Paulo, Brazil
| | | | - Diego Bonaldo Genuário
- University of São Paulo, Center for Nuclear Energy in Agriculture, Avenida Centenário 303, 13400-970 Piracicaba, SP, Brazil
| | - Marli Fatima Fiore
- University of São Paulo, Center for Nuclear Energy in Agriculture, Avenida Centenário 303, 13400-970 Piracicaba, SP, Brazil
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18
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Tang H, Shi X, Wang X, Hao H, Zhang XM, Zhang LP. Environmental Controls Over Actinobacteria Communities in Ecological Sensitive Yanshan Mountains Zone. Front Microbiol 2016; 7:343. [PMID: 27047461 PMCID: PMC4801888 DOI: 10.3389/fmicb.2016.00343] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 03/03/2016] [Indexed: 01/05/2023] Open
Abstract
The Yanshan Mountains are one of the oldest mountain ranges in the world. They are located in an ecologically sensitive zone in northern China near the Hu Huanyong Line. In this metagenomic study, we investigated the diversity of Actinobacteria in soils at 10 sites (YS1–YS10) on the Yanshan Mountains. First, we assessed the effect of different soil prtreatment on Actinobacteria recovery. With the soil pretreatment method: air drying of the soil sample, followed by exposure to 120°C for 1 h, we observed the higher Actinobacteria diversity in a relatively small number of clone libraries. No significant differences were observed in the Actinobacterial diversity of soils from sites YS2, YS3, YS4, YS6, YS8, YS9, or YS10 (P > 0.1). However, there were differences (P < 0.05) from the YS7 site and other sites, especially in response to environmental change. And we observed highly significant differences (P < 0.001) in Actinobacterial diversity of the soil from YS7 and that from YS4 and YS8 sites. The climatic characteristics of mean active accumulated temperature, annual mean precipitation, and annual mean temperature, and biogeochemical data of total phosphorus contributed to the diversity of Actinobacterial communities in soils at YS1, YS3, YS4, and YS5 sites. Compared to the climatic factors, the biogeochemical factors mostly contributed in shaping the Actinobacterial community. This work provides evidence that the diversity of Actinobacterial communities in soils from the Yashan Mountains show regional biogeographic patterns and that community membership change along the north-south distribution of the Hu Huanyong Line.
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Affiliation(s)
- Hui Tang
- College of Life Sciences, Hebei UniversityBaoding, China; The Key Lab of Microbial Diversity Research and Application of Hebei ProvinceBaoding, China; Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Hebei UniversityBaoding, China
| | - Xunxun Shi
- College of Life Sciences, Hebei UniversityBaoding, China; The Key Lab of Microbial Diversity Research and Application of Hebei ProvinceBaoding, China; Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Hebei UniversityBaoding, China
| | - Xiaofei Wang
- College of Life Sciences, Hebei UniversityBaoding, China; The Key Lab of Microbial Diversity Research and Application of Hebei ProvinceBaoding, China; Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Hebei UniversityBaoding, China
| | - Huanhuan Hao
- College of Life Sciences, Hebei UniversityBaoding, China; The Key Lab of Microbial Diversity Research and Application of Hebei ProvinceBaoding, China; Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Hebei UniversityBaoding, China
| | - Xiu-Min Zhang
- College of Life Sciences, Hebei UniversityBaoding, China; The Key Lab of Microbial Diversity Research and Application of Hebei ProvinceBaoding, China; Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Hebei UniversityBaoding, China
| | - Li-Ping Zhang
- College of Life Sciences, Hebei UniversityBaoding, China; The Key Lab of Microbial Diversity Research and Application of Hebei ProvinceBaoding, China; Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Hebei UniversityBaoding, China
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19
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Obbels D, Verleyen E, Mano MJ, Namsaraev Z, Sweetlove M, Tytgat B, Fernandez-Carazo R, De Wever A, D'hondt S, Ertz D, Elster J, Sabbe K, Willems A, Wilmotte A, Vyverman W. Bacterial and eukaryotic biodiversity patterns in terrestrial and aquatic habitats in the Sør Rondane Mountains, Dronning Maud Land, East Antarctica. FEMS Microbiol Ecol 2016; 92:fiw041. [PMID: 26936447 DOI: 10.1093/femsec/fiw041] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/17/2016] [Indexed: 11/12/2022] Open
Abstract
The bacterial and microeukaryotic biodiversity were studied using pyrosequencing analysis on a 454 GS FLX+ platform of partial SSU rRNA genes in terrestrial and aquatic habitats of the Sør Rondane Mountains, including soils, on mosses, endolithic communities, cryoconite holes and supraglacial and subglacial meltwater lenses. This inventory was complemented with Denaturing Gradient Gel Electrophoresis targeting Chlorophyta and Cyanobacteria. OTUs belonging to the Rotifera, Chlorophyta, Tardigrada, Ciliophora, Cercozoa, Fungi, Bryophyta, Bacillariophyta, Collembola and Nematoda were present with a relative abundance of at least 0.1% in the eukaryotic communities. Cyanobacteria, Proteobacteria, Bacteroidetes, Acidobacteria, FBP and Actinobacteria were the most abundant bacterial phyla. Multivariate analyses of the pyrosequencing data revealed a general lack of differentiation of both eukaryotes and prokaryotes according to habitat type. However, the bacterial community structure in the aquatic habitats was dominated by the filamentous cyanobacteria Leptolyngbya and appeared to be significantly different compared with those in dry soils, on mosses, and in endolithic habitats. A striking feature in all datasets was the detection of a relatively large amount of sequences new to science, which underscores the need for additional biodiversity assessments in Antarctic inland locations.
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Affiliation(s)
- Dagmar Obbels
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, Krijgslaan 281, S8, B-9000 Ghent, Belgium
| | - Elie Verleyen
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, Krijgslaan 281, S8, B-9000 Ghent, Belgium
| | - Marie-José Mano
- Centre for Protein Engineering, Institute of Chemistry, Université de Liège, Sart-TilmanB6, B-4000 Liège, Belgium
| | - Zorigto Namsaraev
- Centre for Protein Engineering, Institute of Chemistry, Université de Liège, Sart-TilmanB6, B-4000 Liège, Belgium Winogradsky Institute of Microbiology RAS, Pr-t 60-letya Oktyabrya, 7/2, Moscow 117312, Russia NRC Kurchatov Institute, Akademika Kurchatova pl. 1, Moscow, 12 31 82, Russia
| | - Maxime Sweetlove
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, Krijgslaan 281, S8, B-9000 Ghent, Belgium
| | - Bjorn Tytgat
- Laboratory for Microbiology, Department of Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, 9000 Gent, Belgium
| | - Rafael Fernandez-Carazo
- Centre for Protein Engineering, Institute of Chemistry, Université de Liège, Sart-TilmanB6, B-4000 Liège, Belgium
| | - Aaike De Wever
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, Krijgslaan 281, S8, B-9000 Ghent, Belgium Operational Directorate Natural Environment, Royal Belgian Institute of Natural Sciences, Vautierstraat 29, 1000 Brussels, Belgium
| | - Sofie D'hondt
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, Krijgslaan 281, S8, B-9000 Ghent, Belgium
| | - Damien Ertz
- Botanic Garden Meise, Department Bryophytes-Thallophytes, Nieuwelaan 38, B-1860 Meise, Belgium Federation Wallonia-Brussels, General Administration of the Non-Compulsory Education and Scientific Research, Rue A. Lavallée 1, 1080 Brussels, Belgium
| | - Josef Elster
- Centre for Polar Ecology, Faculty of Sciences, University of South Bohemia, Institute of Botany, Academy of Sciences of the Czech Republic, Dukelská 135, 379 82, Třeboň, Czech republic
| | - Koen Sabbe
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, Krijgslaan 281, S8, B-9000 Ghent, Belgium
| | - Anne Willems
- Laboratory for Microbiology, Department of Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, 9000 Gent, Belgium
| | - Annick Wilmotte
- Centre for Protein Engineering, Institute of Chemistry, Université de Liège, Sart-TilmanB6, B-4000 Liège, Belgium
| | - Wim Vyverman
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, Krijgslaan 281, S8, B-9000 Ghent, Belgium
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20
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Postma A, Slabbert E, Postma F, Jacobs K. Soil bacterial communities associated with natural and commercialCyclopiaspp. FEMS Microbiol Ecol 2016; 92:fiw016. [DOI: 10.1093/femsec/fiw016] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/25/2016] [Indexed: 12/16/2022] Open
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21
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Chrismas NAM, Anesio AM, Sánchez-Baracaldo P. Multiple adaptations to polar and alpine environments within cyanobacteria: a phylogenomic and Bayesian approach. Front Microbiol 2015; 6:1070. [PMID: 26528250 PMCID: PMC4602134 DOI: 10.3389/fmicb.2015.01070] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 09/17/2015] [Indexed: 01/15/2023] Open
Abstract
Cyanobacteria are major primary producers in the polar and alpine regions contributing significantly to nitrogen and carbon cycles in the cryosphere. Recent advancements in environmental sequencing techniques have revealed great molecular diversity of microorganisms in cold environments. However, there are no comprehensive phylogenetic analyses including the entire known diversity of cyanobacteria from these extreme environments. We present here a global phylogenetic analysis of cyanobacteria including an extensive dataset comprised of available small subunit (SSU) rRNA gene sequences of cyanobacteria from polar and high altitude environments. Furthermore, we used a large-scale multi-gene (135 proteins and 2 ribosomal RNAs) genome constraint including 57 cyanobacterial genomes. Our analyses produced the first phylogeny of cold cyanobacteria exhibiting robust deep branching relationships implementing a phylogenomic approach. We recovered several clades common to Arctic, Antarctic and alpine sites suggesting that the traits necessary for survival in the cold have been acquired by a range of different mechanisms in all major cyanobacteria lineages. Bayesian ancestral state reconstruction revealed that 20 clades each have common ancestors with high probabilities of being capable of surviving in cold environments.
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Affiliation(s)
- Nathan A M Chrismas
- Bristol Glaciology Centre, School of Geographical Sciences, University of Bristol Bristol, UK
| | - Alexandre M Anesio
- Bristol Glaciology Centre, School of Geographical Sciences, University of Bristol Bristol, UK
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22
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Ji M, van Dorst J, Bissett A, Brown MV, Palmer AS, Snape I, Siciliano SD, Ferrari BC. Microbial diversity at Mitchell Peninsula, Eastern Antarctica: a potential biodiversity “hotspot”. Polar Biol 2015. [DOI: 10.1007/s00300-015-1776-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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23
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Venkatachalam S, Gowdaman V, Prabagaran SR. Culturable and culture-independent bacterial diversity and the prevalence of cold-adapted enzymes from the Himalayan mountain ranges of India and Nepal. MICROBIAL ECOLOGY 2015; 69:472-91. [PMID: 25204748 DOI: 10.1007/s00248-014-0476-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 07/28/2014] [Indexed: 05/18/2023]
Abstract
Bacterial diversity of soil samples collected from different geographical regions of Himalayan mountains was studied through culturable (13 samples) and culture-independent approaches (5 samples based on abundance of diversity indices in each ecological niche). Shannon-Wiener diversity index and total bacterial count ranged from 1.50 ± 0.1 to 2.57 ± 0.15 and 7.8 ± 1.6 × 10(5) to 30.9 ± 1.7 × 10(5) cfu ml(-1) of soil, respectively. Based on morphology and pigmentation, 406 isolates were selected by culturing in different cultivable media at various strengths and concentrations. All the strains were subjected to amplified ribosomal DNA restriction analysis and the representative isolates from each cluster were chosen for 16S rRNA gene sequence-based identification. Soil habitat in Himalayan foot hills was dominated by the genera Arthrobacter, Exiguobacterium, Bacillus, Cedecea, Erwinia, and Pseudomonas. Five 16S rRNA gene libraries from the selected five samples yielded 268 clones and were grouped into 53 phylotypes covering 25 genera including the genus of Ferribacterium, Rothia, and Wautersiella, which were reported for the first time in Himalayan tracks. Principal coordinates analysis indicates that all the clone libraries were clearly separated and found to be significantly different from each other. Further, extracellular investigation of cold-active enzymes showed activity of cellulase (23.71%), pectinase (20.24%), amylase (17.32%), phytase (13.87%), protease (12.72%), and lipase (23.71%) among the isolates. Four isolates namely Exiguobacterium mexicanum (BSa14), Exiguobacterium sibiricum (BZa11), Micrococcus antarcticus (BSb10), and Bacillus simplex (BZb3) showed multiple enzyme activity for five different types of enzymes. In addition, various genera like Exiguobacterium, Erwinia, Mycetecola, Cedecea, Pantoea, and Trichococcus have also shown novel hydrolytic enzyme activity in the Himalayan foothills.
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Affiliation(s)
- Siddarthan Venkatachalam
- Molecular Microbiology Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, 641046, Tamil Nadu, India
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24
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Rampelotto PH, Barboza ADM, Pereira AB, Triplett EW, Schaefer CEGR, de Oliveira Camargo FA, Roesch LFW. Distribution and interaction patterns of bacterial communities in an ornithogenic soil of Seymour Island, Antarctica. MICROBIAL ECOLOGY 2015; 69:684-694. [PMID: 25342537 DOI: 10.1007/s00248-014-0510-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 10/08/2014] [Indexed: 06/04/2023]
Abstract
Next-generation, culture-independent sequencing offers an excellent opportunity to examine network interactions among different microbial species. In this study, soil bacterial communities from a penguin rookery site at Seymour Island were analyzed for abundance, structure, diversity, and interaction networks to identify interaction patterns among the various taxa at three soil depths. The analysis revealed the presence of eight phyla distributed in different proportions among the surface layer (0-8 cm), middle layer (20-25 cm), and bottom (35-40 cm). The bottom layer presented the highest values of bacterial richness, diversity, and evenness when compared to surface and middle layers. The network analysis revealed the existence of a unique pattern of interactions in which the soil microbial network formed a clustered topology, rather than a modular structure as is usually found in biological communities. In addition, specific taxa were identified as important players in microbial community structure. Furthermore, simulation analyses indicated that the loss of potential keystone groups of microorganisms might alter the patterns of interactions within the microbial community. These findings provide new insights for assessing the consequences of environmental disturbances at the whole-community level in Antarctica.
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Affiliation(s)
- Pabulo Henrique Rampelotto
- Universidade Federal do Pampa, Campus São Gabriel, Av. Antonio Trilha, 1847, 97300-000, São Gabriel, Rio Grande do Sul, Brazil
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25
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Kim M, Cho A, Lim HS, Hong SG, Kim JH, Lee J, Choi T, Ahn TS, Kim OS. Highly heterogeneous soil bacterial communities around Terra Nova Bay of Northern Victoria Land, Antarctica. PLoS One 2015; 10:e0119966. [PMID: 25799273 PMCID: PMC4370865 DOI: 10.1371/journal.pone.0119966] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 01/18/2015] [Indexed: 11/19/2022] Open
Abstract
Given the diminished role of biotic interactions in soils of continental Antarctica, abiotic factors are believed to play a dominant role in structuring of microbial communities. However, many ice-free regions remain unexplored, and it is unclear which environmental gradients are primarily responsible for the variations among bacterial communities. In this study, we investigated the soil bacterial community around Terra Nova Bay of Victoria Land by pyrosequencing and determined which environmental variables govern the bacterial community structure at the local scale. Six bacterial phyla, Actinobacteria, Proteobacteria, Acidobacteria, Chloroflexi, Cyanobacteria, and Bacteroidetes, were dominant, but their relative abundance varied greatly across locations. Bacterial community structures were affected little by spatial distance, but structured more strongly by site, which was in accordance with the soil physicochemical compositions. At both the phylum and species levels, bacterial community structure was explained primarily by pH and water content, while certain earth elements and trace metals also played important roles in shaping community variation. The higher heterogeneity of the bacterial community structure found at this site indicates how soil bacterial communities have adapted to different compositions of edaphic variables under extreme environmental conditions. Taken together, these findings greatly advance our understanding of the adaption of soil bacterial populations to this harsh environment.
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Affiliation(s)
- Mincheol Kim
- Arctic Research Center, Korea Polar Research Institute, Incheon, Republic of Korea
| | - Ahnna Cho
- Division of Life Sciences, Korea Polar Research Institute, Incheon, Republic of Korea
- Department of Environmental Science, Kangwon National University, Chuncheon, Republic of Korea
| | - Hyoun Soo Lim
- Department of Geological Sciences, Pusan National University, Busan, Republic of Korea
| | - Soon Gyu Hong
- Division of Life Sciences, Korea Polar Research Institute, Incheon, Republic of Korea
| | - Ji Hee Kim
- Department of New Antarctic Station, Korea Polar Research Institute, Incheon, Republic of Korea
| | - Joohan Lee
- Department of New Antarctic Station, Korea Polar Research Institute, Incheon, Republic of Korea
| | - Taejin Choi
- Division of Climate Change, Korea Polar Research Institute, Incheon, Republic of Korea
| | - Tae Seok Ahn
- Department of Environmental Science, Kangwon National University, Chuncheon, Republic of Korea
| | - Ok-Sun Kim
- Division of Life Sciences, Korea Polar Research Institute, Incheon, Republic of Korea
- * E-mail:
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26
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Convey P, Chown SL, Clarke A, Barnes DKA, Bokhorst S, Cummings V, Ducklow HW, Frati F, Green TGA, Gordon S, Griffiths HJ, Howard-Williams C, Huiskes AHL, Laybourn-Parry J, Lyons WB, McMinn A, Morley SA, Peck LS, Quesada A, Robinson SA, Schiaparelli S, Wall DH. The spatial structure of Antarctic biodiversity. ECOL MONOGR 2014. [DOI: 10.1890/12-2216.1] [Citation(s) in RCA: 232] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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27
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Bakermans C, Skidmore ML, Douglas S, McKay CP. Molecular characterization of bacteria from permafrost of the Taylor Valley, Antarctica. FEMS Microbiol Ecol 2014; 89:331-46. [DOI: 10.1111/1574-6941.12310] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Revised: 02/18/2014] [Accepted: 02/19/2014] [Indexed: 12/01/2022] Open
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28
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Ex-situ enzyme activity and bacterial community diversity through soil depth profiles in penguin and seal colonies on Vestfold Hills, East Antarctica. Polar Biol 2013. [DOI: 10.1007/s00300-013-1355-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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29
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Distinct soil bacterial communities revealed under a diversely managed agroecosystem. PLoS One 2012; 7:e40338. [PMID: 22844402 PMCID: PMC3402512 DOI: 10.1371/journal.pone.0040338] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Accepted: 06/06/2012] [Indexed: 12/29/2022] Open
Abstract
Land-use change and management practices are normally enacted to manipulate environments to improve conditions that relate to production, remediation, and accommodation. However, their effect on the soil microbial community and their subsequent influence on soil function is still difficult to quantify. Recent applications of molecular techniques to soil biology, especially the use of 16S rRNA, are helping to bridge this gap. In this study, the influence of three land-use systems within a demonstration farm were evaluated with a view to further understand how these practices may impact observed soil bacterial communities. Replicate soil samples collected from the three land-use systems (grazed pine forest, cultivated crop, and grazed pasture) on a single soil type. High throughput 16S rRNA gene pyrosequencing was used to generate sequence datasets. The different land use systems showed distinction in the structure of their bacterial communities with respect to the differences detected in cluster analysis as well as diversity indices. Specific taxa, particularly Actinobacteria, Acidobacteria, and classes of Proteobacteria, showed significant shifts across the land-use strata. Families belonging to these taxa broke with notions of copio- and oligotrphy at the class level, as many of the less abundant groups of families of Actinobacteria showed a propensity for soil environments with reduced carbon/nutrient availability. Orders Actinomycetales and Solirubrobacterales showed their highest abundance in the heavily disturbed cultivated system despite the lowest soil organic carbon (SOC) values across the site. Selected soil properties ([SOC], total nitrogen [TN], soil texture, phosphodiesterase [PD], alkaline phosphatase [APA], acid phosphatase [ACP] activity, and pH) also differed significantly across land-use regimes, with SOM, PD, and pH showing variation consistent with shifts in community structure and composition. These results suggest that use of pyrosequencing along with traditional analysis of soil physiochemical properties may provide insight into the ecology of descending taxonomic groups in bacterial communities.
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