101
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Li L, Lin Q, Li X, Li T, He X, Li D, Tao Y. Dynamics and potential roles of abundant and rare subcommunities in the bioremediation of cadmium-contaminated paddy soil by Pseudomonas chenduensis. Appl Microbiol Biotechnol 2019; 103:8203-8214. [PMID: 31396678 DOI: 10.1007/s00253-019-10059-y] [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: 05/06/2019] [Revised: 07/08/2019] [Accepted: 07/22/2019] [Indexed: 10/26/2022]
Abstract
Microbial bioremediation of heavy metal-contaminated soil is a potential technique to reduce heavy metals in crop plants. However, the dynamics and roles of the local microbiota in bioremediation of heavy metal-contaminated soil following microbial application are rarely reported. In this study, we used Pseudomonas chenduensis strain MBR for bioremediation of Cd-contaminated paddy soil and investigated its effects on the dynamics of the local soil bacterial community and Cd accumulation in rice. Cd accumulation in rice grains and roots were significantly reduced by the addition of the strain MBR. The addition of the strain MBR caused greater changes in bacterial communities in rhizosphere soil than in bulk soil. MBR enhanced the roles of microbial communities in transformation of Cd fractions, especially in rhizosphere soil. The strain MBR likely regulated abundant subcommunities more than rare subcommunities to improve Cd bioremediation, especially in rhizosphere soil. Consequently, the dynamics and functional roles of the local microbial communities differed significantly during bioremediation between abundant and rare subcommunities and between rhizosphere soil and bulk soil. This study provides new insight into the microbiota-related mechanisms underlying bioremediation.
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Affiliation(s)
- Lingjuan Li
- Key Laboratory of Environmental and Applied Microbiology, CAS & Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Qiang Lin
- Biology Centre of the Czech Academy of Sciences, Institute of Soil Biology & SoWa Research Infrastructure, Na Sádkách 7, 37005, České Budějovice, Czech Republic
| | - Xiangzhen Li
- Key Laboratory of Environmental and Applied Microbiology, CAS & Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Tiezhu Li
- Key Laboratory of Environmental and Applied Microbiology, CAS & Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Xiaohong He
- Key Laboratory of Environmental and Applied Microbiology, CAS & Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Daping Li
- Key Laboratory of Environmental and Applied Microbiology, CAS & Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Yong Tao
- Key Laboratory of Environmental and Applied Microbiology, CAS & Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.
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102
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Sato Y, Hamai T, Hori T, Aoyagi T, Inaba T, Kobayashi M, Habe H, Sakata T. Desulfosporosinus spp. were the most predominant sulfate-reducing bacteria in pilot- and laboratory-scale passive bioreactors for acid mine drainage treatment. Appl Microbiol Biotechnol 2019; 103:7783-7793. [DOI: 10.1007/s00253-019-10063-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 07/22/2019] [Accepted: 07/24/2019] [Indexed: 11/29/2022]
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103
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Liu J, Yao J, Sunahara G, Wang F, Li Z, Duran R. Nonferrous metal (loid) s mediate bacterial diversity in an abandoned mine tailing impoundment. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:24806-24818. [PMID: 31240654 DOI: 10.1007/s11356-019-05092-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Accepted: 04/04/2019] [Indexed: 06/09/2023]
Abstract
Migration and transformation of toxic metal (loid) s in tailing sites inevitably lead to ecological disturbances and serious threats to the surroundings. However, the horizontal and vertical distribution of bacterial diversity has not been determined in nonferrous metal (loid) tailing ponds, especially in Guangxi China, where the world's largest and potentially most toxic sources of metal (loid) s are located. Distribution of bacterial communities was stable at horizontal levels. At the surface (0-10 cm), the stability was most attributed to Bacillus and Enterococcus, while bacterial communities at the subsurface (50 cm) were mainly contributed by Nitrospira and Sulfuricella. Variable vertical distribution of bacterial communities has led to the occurrence of specific genera and specific predicted functions (such as transcription regulation factors). Sulfurifustis (a S-oxidizing and inorganic carbon fixing bacteria) genera were specific at the surface, whereas Streptococcus-related genera were found at the surface and subsurface, but were more abundant in the latter depth. Physical-chemical parameters, such as pH, TN, and metal (loid) (As, Cd, Pb, Cu, and Zn) concentrations were the main drivers of bacterial community abundance, diversity, composition, and metabolic functions. These results increase our understanding of the physical-chemical effects on the spatial distribution of bacterial communities and provide useful insight for the bioremediation and site management of nonferrous metal (loid) tailings.
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Affiliation(s)
- Jianli Liu
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Jun Yao
- School of Water Resource and Environment Engineering, Research Center of Environmental Sciences and Engineering, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing, 100083, China.
| | - Geoffrey Sunahara
- School of Water Resource and Environment Engineering, Research Center of Environmental Sciences and Engineering, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing, 100083, China
- Department of Natural Resource Sciences, McGill University, Montreal, H9X3V9, Quebec, Canada
| | - Fei Wang
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Zifu Li
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, China.
| | - Robert Duran
- School of Water Resource and Environment Engineering, Research Center of Environmental Sciences and Engineering, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing, 100083, China
- Equipe Environnement et Microbiologie, MELODY group, Université de Pau et des Pays de l'Adour, IPREM UMR CNRS 5254, BP 1155, 64013, Pau, Cedex, France
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104
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Draft Genome Sequence of Desulfosporosinus sp. Strain Sb-LF, Isolated from an Acidic Peatland in Germany. Microbiol Resour Announc 2019; 8:8/29/e00428-19. [PMID: 31320430 PMCID: PMC6639609 DOI: 10.1128/mra.00428-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Desulfosporosinus sp. strain Sb-LF was isolated from an acidic peatland in Bavaria, Germany. Here, we report the draft genome sequence of the sulfate-reducing and lactate-utilizing strain Sb-LF. Desulfosporosinus sp. strain Sb-LF was isolated from an acidic peatland in Bavaria, Germany. Here, we report the draft genome sequence of the sulfate-reducing and lactate-utilizing strain Sb-LF.
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105
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Liu JL, Yao J, Lu C, Li H, Li ZF, Duran R, Sunahara G, Mihucz VG. Microbial activity and biodiversity responding to contamination of metal(loid) in heterogeneous nonferrous mining and smelting areas. CHEMOSPHERE 2019; 226:659-667. [PMID: 30959450 DOI: 10.1016/j.chemosphere.2019.03.051] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 02/28/2019] [Accepted: 03/10/2019] [Indexed: 06/09/2023]
Abstract
The combined contamination of nonferrous metal(loid) mining and smelting areas is a global issue, in need of urgent management. To our knowledge, this is the first report of microbial activities by microcalorimetry in specific nonferrous metal(loid) tailings with oligonutrition and high contents of toxic metal(loid)s. Dynamics of bacterial diversity were also characterized. Here we show that tailings had low microbial activities (Pmax = 64.1-331 μW g-1), which were accelerated by the presence of dipotassium phosphate (Pmax = 346-856 μW g-1), as measured by microcalorimetry. Frequent detection of S- and metal-resistant related genera and differences of Thiobacillus and Acidithiobacillus abundances indicated that the tailings were in an early stage of acidification. It has been further confirmed by the presence of a weak acid environment and secondary sulfur associated minerals, such as Sb2S3, FeAsS, FeS2, and CuFeS2. During the acidification process, phosphate, metal(loid)s, and microbial activity were correlated to the bacterial communities. It is suggested that the bacterial communities have metabolic capacities with a high potential for the use in management processes of multi-contaminated nonferrous metalliferous tailings.
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Affiliation(s)
- Jian-Li Liu
- School of Energy and Environment Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Jun Yao
- School of Water Resource and Environment Engineering, Research Center of Environmental Sciences and Engineering, China University of Geosciences (Beijing), 100083, China.
| | - Chao Lu
- School of Water Resource and Environment Engineering, Research Center of Environmental Sciences and Engineering, China University of Geosciences (Beijing), 100083, China
| | - Hao Li
- School of Water Resource and Environment Engineering, Research Center of Environmental Sciences and Engineering, China University of Geosciences (Beijing), 100083, China
| | - Zi-Fu Li
- School of Energy and Environment Engineering, University of Science and Technology Beijing, Beijing, 100083, China.
| | - Robert Duran
- School of Water Resource and Environment Engineering, Research Center of Environmental Sciences and Engineering, China University of Geosciences (Beijing), 100083, China; Equipe Environnement et Microbiologie, MELODY Group, Université de Pau et des Pays de l'Adour, E2S-UPPA, IPREM UMR CNRS 5254, BP 1155, 64013, Pau Cedex, France
| | - Geoffrey Sunahara
- School of Water Resource and Environment Engineering, Research Center of Environmental Sciences and Engineering, China University of Geosciences (Beijing), 100083, China; Department of Natural Resource Sciences, McGill University, 21111, Lakeshore Drive, Ste-Anne-de-Bellevue, Quebec, H9X 3V9, Canada
| | - Victor G Mihucz
- Sino-Hungarian Joint Research Laboratory for Environmental Sciences and Health, ELTE -Eötvös Loránd University, H-1117, Budapest, Pázmány Péter stny. 1/A, Hungary
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106
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Lee SA, Kim Y, Kim JM, Chu B, Joa JH, Sang MK, Song J, Weon HY. A preliminary examination of bacterial, archaeal, and fungal communities inhabiting different rhizocompartments of tomato plants under real-world environments. Sci Rep 2019; 9:9300. [PMID: 31243310 PMCID: PMC6594962 DOI: 10.1038/s41598-019-45660-8] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 06/10/2019] [Indexed: 01/21/2023] Open
Abstract
Plant microbiota is a key determinant of plant health and productivity. The composition and structure of plant microbiota varies according to plant tissue and compartment, which are specific habitats for microbial colonization. To investigate the structural composition of the microbiome associated with tomato roots under natural systems, we characterized the bacterial, archaeal, and fungal communities of three belowground compartments (rhizosphere, endosphere, and bulk soil) of tomato plants collected from 23 greenhouses in 7 geographic locations of South Korea. The microbial diversity and structure varied by rhizocompartment, with the most distinctive community features found in the endosphere. The bacterial and fungal communities in the bulk soil and rhizosphere were correlated with soil physicochemical properties, such as pH, electrical conductivity, and exchangeable cation levels, while this trend was not evident in the endosphere samples. A small number of core bacterial operational taxonomic units (OTUs) present in all samples from the rhizosphere and endosphere represented more than 60% of the total relative abundance. Among these core microbes, OTUs belonging to the genera Acidovorax, Enterobacter, Pseudomonas, Rhizobium, Streptomyces, and Variovorax, members of which are known to have beneficial effects on plant growth, were more relatively abundant in the endosphere samples. A co-occurrence network analysis indicated that the microbial community in the rhizosphere had a larger and more complex network than those in the bulk soil and endosphere. The analysis also identified keystone taxa that might play important roles in microbe-microbe interactions in the community. Additionally, profiling of predicted gene functions identified many genes associated with membrane transport in the endospheric and rhizospheric communities. Overall, the data presented here provide preliminary insight into bacterial, archaeal, and fungal phylogeny, functionality, and interactions in the rhizocompartments of tomato roots under real-world environments.
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Affiliation(s)
- Shin Ae Lee
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Wanju, 55365, South Korea
| | - Yiseul Kim
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Wanju, 55365, South Korea
| | - Jeong Myeong Kim
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Wanju, 55365, South Korea
| | - Bora Chu
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Wanju, 55365, South Korea
| | - Jae-Ho Joa
- Research Institute of Climate Change and Agriculture, National Institute of Horticultural & Herbal Science, RDA, Jeju, 63240, South Korea
| | - Mee Kyung Sang
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Wanju, 55365, South Korea
| | - Jaekyeong Song
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Wanju, 55365, South Korea
| | - Hang-Yeon Weon
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Wanju, 55365, South Korea.
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107
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Hogan G, Walker S, Turnbull F, Curiao T, Morrison AA, Flores Y, Andrews L, Claesson MJ, Tangney M, Bartley DJ. Microbiome analysis as a platform R&D tool for parasitic nematode disease management. ISME JOURNAL 2019; 13:2664-2680. [PMID: 31239540 DOI: 10.1038/s41396-019-0462-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 05/06/2019] [Accepted: 06/06/2019] [Indexed: 12/16/2022]
Abstract
The relationship between bacterial communities and their host is being extensively investigated for the potential to improve the host's health. Little is known about the interplay between the microbiota of parasites and the health of the infected host. Using nematode co-infection of lambs as a proof-of-concept model, the aim of this study was to characterise the microbiomes of nematodes and that of their host, enabling identification of candidate nematode-specific microbiota member(s) that could be exploited as drug development tools or for targeted therapy. Deep sequencing techniques were used to elucidate the microbiomes of different life stages of two parasitic nematodes of ruminants, Haemonchus contortus and Teladorsagia circumcincta, as well as that of the co-infected ovine hosts, pre- and post infection. Bioinformatic analyses demonstrated significant differences between the composition of the nematode and ovine microbiomes. The two nematode species also differed significantly. The data indicated a shift in the constitution of the larval nematode microbiome after exposure to the ovine microbiome, and in the ovine intestinal microbial community over time as a result of helminth co-infection. Several bacterial species were identified in nematodes that were absent from their surrounding abomasal environment, the most significant of which included Escherichia coli/Shigella. The ability to purposefully infect nematode species with engineered E. coli was demonstrated in vitro, validating the concept of using this bacterium as a nematode-specific drug development tool and/or drug delivery vehicle. To our knowledge, this is the first description of the concept of exploiting a parasite's microbiome for drug development and treatment purposes.
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Affiliation(s)
- Glenn Hogan
- SynBioCentre, University College Cork, Cork, Ireland.,Cancer Research@UCC, University College Cork, Cork, Ireland
| | - Sidney Walker
- SynBioCentre, University College Cork, Cork, Ireland.,Cancer Research@UCC, University College Cork, Cork, Ireland.,APC Microbiome Ireland, University College Cork, Cork, Ireland.,Department of Microbiology, University College Cork, Cork, Ireland
| | - Frank Turnbull
- Moredun Research Institute, Pentlands Science Park, Penicuik, EH26 0PZ, UK
| | - Tania Curiao
- SynBioCentre, University College Cork, Cork, Ireland.,Cancer Research@UCC, University College Cork, Cork, Ireland
| | - Alison A Morrison
- Moredun Research Institute, Pentlands Science Park, Penicuik, EH26 0PZ, UK
| | - Yensi Flores
- SynBioCentre, University College Cork, Cork, Ireland.,Cancer Research@UCC, University College Cork, Cork, Ireland.,APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Leigh Andrews
- Moredun Research Institute, Pentlands Science Park, Penicuik, EH26 0PZ, UK
| | - Marcus J Claesson
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,Department of Microbiology, University College Cork, Cork, Ireland
| | - Mark Tangney
- SynBioCentre, University College Cork, Cork, Ireland. .,Cancer Research@UCC, University College Cork, Cork, Ireland. .,APC Microbiome Ireland, University College Cork, Cork, Ireland.
| | - Dave J Bartley
- Moredun Research Institute, Pentlands Science Park, Penicuik, EH26 0PZ, UK.
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108
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Sato Y, Hori T, Koike H, Navarro RR, Ogata A, Habe H. Transcriptome analysis of activated sludge microbiomes reveals an unexpected role of minority nitrifiers in carbon metabolism. Commun Biol 2019; 2:179. [PMID: 31098412 PMCID: PMC6513846 DOI: 10.1038/s42003-019-0418-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 04/05/2019] [Indexed: 12/26/2022] Open
Abstract
Although metagenomics researches have illuminated microbial diversity in numerous biospheres, understanding individual microbial functions is yet difficult due to the complexity of ecosystems. To address this issue, we applied a metagenome-independent, de novo assembly-based metatranscriptomics to a complex microbiome, activated sludge, which has been used for wastewater treatment for over a century. Even though two bioreactors were operated under the same conditions, their performances differed from each other with unknown causes. Metatranscriptome profiles in high- and low-performance reactors demonstrated that denitrifiers contributed to the anaerobic degradation of heavy oil; however, no marked difference in the gene expression was found. Instead, gene expression-based nitrification activities that fueled the denitrifiers by providing the respiratory substrate were notably high in the high-performance reactor only. Nitrifiers-small minorities with relative abundances of <0.25%-governed the heavy-oil degradation performances of the reactors, unveiling an unexpected linkage of carbon- and nitrogen-metabolisms of the complex microbiome.
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Affiliation(s)
- Yuya Sato
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology, 16-1 Onogawa, Tsukuba, Ibaraki 305-8569 Japan
| | - Tomoyuki Hori
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology, 16-1 Onogawa, Tsukuba, Ibaraki 305-8569 Japan
| | - Hideaki Koike
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565 Japan
| | - Ronald R. Navarro
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology, 16-1 Onogawa, Tsukuba, Ibaraki 305-8569 Japan
| | - Atsushi Ogata
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology, 16-1 Onogawa, Tsukuba, Ibaraki 305-8569 Japan
| | - Hiroshi Habe
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology, 16-1 Onogawa, Tsukuba, Ibaraki 305-8569 Japan
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109
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Karikari-Yeboah O, Skinner W, Addai-Mensah J. Anaerobic pyrite oxidation in a naturally occurring pyrite-rich sediment under preload surcharge. ENVIRONMENTAL MONITORING AND ASSESSMENT 2019; 191:216. [PMID: 30868246 DOI: 10.1007/s10661-019-7289-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 02/01/2019] [Indexed: 06/09/2023]
Abstract
Pyrite undergoes oxidation when exposed to aqueous oxygen to produce acidic leachate with high concentrations of H+, SO42-, and Fe3+. The oxidation mechanism is currently ascribed to contact between the mineral and aqueous oxygen. Consequently, management of acidic leachate from acid sulfate soils and acid mine drainage is focused on the prevention of contact between the sediment and aqueous oxygen through the surface. Intriguing though is the fact that in aquatic sediments, redox processes occur in sequence with the oxidizing agents. Among the common oxidants in aquatic sediments are O2, [Formula: see text], Mn, and Fe, in the order of efficiency. Consequently, following the depletion of oxygen in pyrite-rich sediment, it would be expected that [Formula: see text], followed by Mn and then Fe, would continue the oxidation process. However, evidence of anaerobic pyrite oxidation in a naturally occurring pyrite-rich sediment is limited. Few studies have investigated the process in aquatic systems but mostly in laboratory experimental set ups. In this study, pyrite oxidation in a naturally occurring pyrite-rich sediment was investigated. A section of the sediment was covered with surface surcharge, in the form of compacted fill. The section of the sediment outside the surcharged area was preserved and used as control experiment. Solid phase soil and porewater samples were subjected to elemental, mineralogical, and microbial analyses. The results show excess accumulation of sulfate and sulfide in the anoxic zones of the original sediment and beneath the surcharge, accompanied by the disappearance of [Formula: see text], Mn, and Fe in the anoxic zones, indicating electron transfers between donors and acceptors, with pyrite as the most likely electron donor. The study outcome poses a significant challenge to the use of surface cover for the management of acidic leachate from pyrite oxidation, particularly, in areas rich in [Formula: see text], MnO-2, or Fe.
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Affiliation(s)
- O Karikari-Yeboah
- Maiden Geotechnics, P.O. Box 2079, Nerang East, Gold Coast, Queensland, 4211, Australia.
| | - W Skinner
- Future Industries Institute, University of South Australia, Mawson Lakes Campus, Adelaide, South Australia
| | - J Addai-Mensah
- Future Industries Institute, University of South Australia, Mawson Lakes Campus, Adelaide, South Australia
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110
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Wegner CE, Gaspar M, Geesink P, Herrmann M, Marz M, Küsel K. Biogeochemical Regimes in Shallow Aquifers Reflect the Metabolic Coupling of the Elements Nitrogen, Sulfur, and Carbon. Appl Environ Microbiol 2019; 85:e02346-18. [PMID: 30578263 PMCID: PMC6384109 DOI: 10.1128/aem.02346-18] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 12/14/2018] [Indexed: 11/20/2022] Open
Abstract
Near-surface groundwaters are prone to receive (in)organic matter input from their recharge areas and are known to harbor autotrophic microbial communities linked to nitrogen and sulfur metabolism. Here, we use multi-omic profiling to gain holistic insights into the turnover of inorganic nitrogen compounds, carbon fixation processes, and organic matter processing in groundwater. We sampled microbial biomass from two superimposed aquifers via monitoring wells that follow groundwater flow from its recharge area through differences in hydrogeochemical settings and land use. Functional profiling revealed that groundwater microbiomes are mainly driven by nitrogen (nitrification, denitrification, and ammonium oxidation [anammox]) and to a lesser extent sulfur cycling (sulfur oxidation and sulfate reduction), depending on local hydrochemical differences. Surprisingly, the differentiation potential of the groundwater microbiome surpasses that of hydrochemistry for individual monitoring wells. Being dominated by a few phyla (Bacteroidetes, Proteobacteria, Planctomycetes, and Thaumarchaeota), the taxonomic profiling of groundwater metagenomes and metatranscriptomes revealed pronounced differences between merely present microbiome members and those actively participating in community gene expression and biogeochemical cycling. Unexpectedly, we observed a constitutive expression of carbohydrate-active enzymes encoded by different microbiome members, along with the groundwater flow path. The turnover of organic carbon apparently complements for lithoautotrophic carbon assimilation pathways mainly used by the groundwater microbiome depending on the availability of oxygen and inorganic electron donors, like ammonium.IMPORTANCE Groundwater is a key resource for drinking water production and irrigation. The interplay between geological setting, hydrochemistry, carbon storage, and groundwater microbiome ecosystem functioning is crucial for our understanding of these important ecosystem services. We targeted the encoded and expressed metabolic potential of groundwater microbiomes along an aquifer transect that diversifies in terms of hydrochemistry and land use. Our results showed that the groundwater microbiome has a higher spatial differentiation potential than does hydrochemistry.
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Affiliation(s)
- Carl-Eric Wegner
- Chair of Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University, Jena, Germany
| | - Michael Gaspar
- Chair of Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University, Jena, Germany
- RNA Bioinformatics and High-Throughput Analysis, Faculty of Mathematics and Computer Science, Friedrich Schiller University, Jena, Germany
| | - Patricia Geesink
- Chair of Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University, Jena, Germany
| | - Martina Herrmann
- Chair of Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University, Jena, Germany
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Manja Marz
- RNA Bioinformatics and High-Throughput Analysis, Faculty of Mathematics and Computer Science, Friedrich Schiller University, Jena, Germany
- Leibniz Institute on Aging, Fritz Lipman Institute, Jena, Germany
| | - Kirsten Küsel
- Chair of Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University, Jena, Germany
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
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111
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Quantifying population-specific growth in benthic bacterial communities under low oxygen using H 218O. ISME JOURNAL 2019; 13:1546-1559. [PMID: 30783213 PMCID: PMC6776007 DOI: 10.1038/s41396-019-0373-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 01/26/2019] [Accepted: 01/31/2019] [Indexed: 01/09/2023]
Abstract
The benthos in estuarine environments often experiences periods of regularly occurring hypoxic and anoxic conditions, dramatically impacting biogeochemical cycles. How oxygen depletion affects the growth of specific uncultivated microbial populations within these diverse benthic communities, however, remains poorly understood. Here, we applied H218O quantitative stable isotope probing (qSIP) in order to quantify the growth of diverse, uncultured bacterial populations in response to low oxygen concentrations in estuarine sediments. Over the course of 7- and 28-day incubations with redox conditions spanning from hypoxia to euxinia (sulfidic), 18O labeling of bacterial populations exhibited different patterns consistent with micro-aerophilic, anaerobic, facultative anaerobic, and aerotolerant anaerobic growth. 18O-labeled populations displaying anaerobic growth had a significantly non-random phylogenetic distribution, exhibited by numerous clades currently lacking cultured representatives within the Planctomycetes, Actinobacteria, Latescibacteria, Verrucomicrobia, and Acidobacteria. Genes encoding the beta-subunit of the dissimilatory sulfate reductase (dsrB) became 18O labeled only during euxinic conditions. Sequencing of these 18O-labeled dsrB genes showed that Acidobacteria were the dominant group of growing sulfate-reducing bacteria, highlighting their importance for sulfur cycling in estuarine sediments. Our findings provide the first experimental constraints on the redox conditions underlying increased growth in several groups of "microbial dark matter", validating hypotheses put forth by earlier metagenomic studies.
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112
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Hausmann B, Pelikan C, Rattei T, Loy A, Pester M. Long-Term Transcriptional Activity at Zero Growth of a Cosmopolitan Rare Biosphere Member. mBio 2019; 10:e02189-18. [PMID: 30755506 PMCID: PMC6372793 DOI: 10.1128/mbio.02189-18] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 01/04/2019] [Indexed: 01/05/2023] Open
Abstract
Microbial diversity in the environment is mainly concealed within the rare biosphere (all species with <0.1% relative abundance). While dormancy explains a low-abundance state very well, the mechanisms leading to rare but active microorganisms remain elusive. We used environmental systems biology to genomically and transcriptionally characterize "Candidatus Desulfosporosinus infrequens," a low-abundance sulfate-reducing microorganism cosmopolitan to freshwater wetlands, where it contributes to cryptic sulfur cycling. We obtained its near-complete genome by metagenomics of acidic peat soil. In addition, we analyzed anoxic peat soil incubated under in situ-like conditions for 50 days by Desulfosporosinus-targeted qPCR and metatranscriptomics. The Desulfosporosinus population stayed at a constant low abundance under all incubation conditions, averaging 1.2 × 106 16S rRNA gene copies per cm³ soil. In contrast, transcriptional activity of "Ca. Desulfosporosinus infrequens" increased at day 36 by 56- to 188-fold when minor amendments of acetate, propionate, lactate, or butyrate were provided with sulfate, compared to the no-substrate-control. Overall transcriptional activity was driven by expression of genes encoding ribosomal proteins, energy metabolism, and stress response but not by expression of genes encoding cell growth-associated processes. Since our results did not support growth of these highly active microorganisms in terms of biomass increase or cell division, they had to invest their sole energy for maintenance, most likely counterbalancing acidic pH conditions. This finding explains how a rare biosphere member can contribute to a biogeochemically relevant process while remaining in a zero-growth state over a period of 50 days.IMPORTANCE The microbial rare biosphere represents the largest pool of biodiversity on Earth and constitutes, in sum of all its members, a considerable part of a habitat's biomass. Dormancy or starvation is typically used to explain the persistence of low-abundance microorganisms in the environment. We show that a low-abundance microorganism can be highly transcriptionally active while remaining in a zero-growth state for at least 7 weeks. Our results provide evidence that this zero growth at a high cellular activity state is driven by maintenance requirements. We show that this is true for a microbial keystone species, in particular a cosmopolitan but permanently low-abundance sulfate-reducing microorganism in wetlands that is involved in counterbalancing greenhouse gas emissions. In summary, our results provide an important step forward in understanding time-resolved activities of rare biosphere members relevant for ecosystem functions.
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Affiliation(s)
- Bela Hausmann
- Research Network Chemistry meets Microbiology, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Claus Pelikan
- Research Network Chemistry meets Microbiology, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Thomas Rattei
- Research Network Chemistry meets Microbiology, Department of Microbiology and Ecosystem Science, Division of Computational Systems Biology, University of Vienna, Vienna, Austria
| | - Alexander Loy
- Research Network Chemistry meets Microbiology, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Michael Pester
- Department of Biology, University of Konstanz, Konstanz, Germany
- Department of Microorganisms, Leibniz Institute DSMZ, Braunschweig, Germany
- Institute of Microbiology, Technical University of Braunschweig, Braunschweig, Germany
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113
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Ma M, Du H, Sun T, An S, Yang G, Wang D. Characteristics of archaea and bacteria in rice rhizosphere along a mercury gradient. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 650:1640-1651. [PMID: 30054090 DOI: 10.1016/j.scitotenv.2018.07.175] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 07/10/2018] [Accepted: 07/13/2018] [Indexed: 06/08/2023]
Abstract
Several strains of archaea have the ability to methylate or resist mercury (Hg), and the paddy field is regarded to be conducive to Hg methylation. However, our knowledge of Hg-methylating or Hg-resistant archaea in paddy soils is very limited so far. Therefore, the distribution of archaea and bacteria in the rhizosphere (RS) and bulk soil (BS) of the rice growing in Xiushan Hg-mining area of southwest China was investigated. Bacterial and archaeal 16S rRNA gene amplicon sequencing of the rice rhizosphere along the Hg gradient was conducted. THg concentrations in RS were significantly higher than that in BS at site S1 and S2, while MeHg concentrations in RS was always higher than that in BS, except S6. Bacterial species richness estimates were much higher than that in archaea. The bacterial α-diversity in high-Hg sites was significant higher than that in low-Hg sites based on ACE and Shannon indices. At the genus level, Thiobacillus, Xanthomonas, Defluviicoccus and Candidatus Nitrosoarchaeum were significantly more abundant in the rhizosphere of high-Hg sites, which meant that strains in these genera might play important roles in response to Hg stress. Hg-methylating archaea in the paddy field could potentially be affiliated to strains in Methanosarcina, but further evidence need to be found. The results provide reference to understand archaeal rhizosphere community along an Hg gradient paddy soils.
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Affiliation(s)
- Ming Ma
- College of Resources and Environment, Southwest University, Chongqing 400715, China; School of Environment, Jinan University, Guangzhou 510632, China
| | - Hongxia Du
- College of Resources and Environment, Southwest University, Chongqing 400715, China; Research Center of Bioenergy and Bioremediation, Southwest University, Chongqing 400715, China
| | - Tao Sun
- College of Resources and Environment, Southwest University, Chongqing 400715, China
| | - Siwei An
- College of Resources and Environment, Southwest University, Chongqing 400715, China
| | - Guang Yang
- College of Resources and Environment, Southwest University, Chongqing 400715, China
| | - Dingyong Wang
- College of Resources and Environment, Southwest University, Chongqing 400715, China.
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114
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Ueki T, Fujie M, Romaidi, Satoh N. Symbiotic bacteria associated with ascidian vanadium accumulation identified by 16S rRNA amplicon sequencing. Mar Genomics 2019; 43:33-42. [DOI: 10.1016/j.margen.2018.10.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 10/10/2018] [Accepted: 10/29/2018] [Indexed: 01/31/2023]
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115
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Hu D, Zhang S, Baskin JM, Baskin CC, Wang Z, Liu R, Du J, Yang X, Huang Z. Seed mucilage interacts with soil microbial community and physiochemical processes to affect seedling emergence on desert sand dunes. PLANT, CELL & ENVIRONMENT 2019; 42:591-605. [PMID: 30193400 DOI: 10.1111/pce.13442] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 08/31/2018] [Accepted: 09/03/2018] [Indexed: 06/08/2023]
Abstract
Seedling emergence is a critical stage in the establishment of desert plants. Soil microbes participate in plant growth and development, but information is lacking with regard to the role of microbes on seedling emergence. We applied the biocides (captan and streptomycin) to assess how seed mucilage interacts with soil microbial community and physiochemical processes to affect seedling emergence of Artemisia sphaerocephala on the desert sand dune. Fungal and bacterial community composition and diversity and fungal-bacterial interactions were changed by both captan and streptomycin. Mucilage increased soil enzyme activities and fungal-bacterial interactions. Highest seedling emergence occurred under streptomycin and mucilage treatment. Members of the phyla Firmicutes and Glomeromycota were the keystone species that improved A. sphaerocephala seedling emergence, by increasing resistance of young seedlings to drought and pathogen. Seed mucilage directly improved seedling emergence and indirectly interacted with the soil microbial community through strengthening fungal-bacterial interactions and providing favourable environment for soil enzymes to affect seedling emergence. Our study provides a comprehensive understanding of the regulatory mechanisms by which soil microbial community and seed mucilage interactively promote successful establishment of populations of desert plants on the barren and stressful sand dune.
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Affiliation(s)
- Dandan Hu
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shudong Zhang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jerry M Baskin
- Department of Biology, University of Kentucky, Lexington, Kentucky
| | - Carol C Baskin
- Department of Biology, University of Kentucky, Lexington, Kentucky
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, Kentucky
| | - Zhaoren Wang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Rong Liu
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Juan Du
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Xuejun Yang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Zhenying Huang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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116
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Mercury methylating microbial communities of boreal forest soils. Sci Rep 2019; 9:518. [PMID: 30679728 PMCID: PMC6345997 DOI: 10.1038/s41598-018-37383-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 11/29/2018] [Indexed: 02/05/2023] Open
Abstract
The formation of the potent neurotoxic methylmercury (MeHg) is a microbially mediated process that has raised much concern because MeHg poses threats to wildlife and human health. Since boreal forest soils can be a source of MeHg in aquatic networks, it is crucial to understand the biogeochemical processes involved in the formation of this pollutant. High-throughput sequencing of 16S rRNA and the mercury methyltransferase, hgcA, combined with geochemical characterisation of soils, were used to determine the microbial populations contributing to MeHg formation in forest soils across Sweden. The hgcA sequences obtained were distributed among diverse clades, including Proteobacteria, Firmicutes, and Methanomicrobia, with Deltaproteobacteria, particularly Geobacteraceae, dominating the libraries across all soils examined. Our results also suggest that MeHg formation is also linked to the composition of non-mercury methylating bacterial communities, likely providing growth substrate (e.g. acetate) for the hgcA-carrying microorganisms responsible for the actual methylation process. While previous research focused on mercury methylating microbial communities of wetlands, this study provides some first insights into the diversity of mercury methylating microorganisms in boreal forest soils.
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117
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Thiel V, Garcia Costas AM, Fortney NW, Martinez JN, Tank M, Roden EE, Boyd ES, Ward DM, Hanada S, Bryant DA. " Candidatus Thermonerobacter thiotrophicus," A Non-phototrophic Member of the Bacteroidetes/Chlorobi With Dissimilatory Sulfur Metabolism in Hot Spring Mat Communities. Front Microbiol 2019; 9:3159. [PMID: 30687241 PMCID: PMC6338057 DOI: 10.3389/fmicb.2018.03159] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 12/05/2018] [Indexed: 12/31/2022] Open
Abstract
In this study we present evidence for a novel, thermophilic bacterium with dissimilatory sulfur metabolism, tentatively named “Candidatus Thermonerobacter thiotrophicus,” which is affiliated with the Bacteroides/Ignavibacteria/Chlorobi and which we predict to be a sulfate reducer. Dissimilatory sulfate reduction (DSR) is an important and ancient metabolic process for energy conservation with global importance for geochemical sulfur and carbon cycling. Characterized sulfate-reducing microorganisms (SRM) are found in a limited number of bacterial and archaeal phyla. However, based on highly diverse environmental dsrAB sequences, a variety of uncultivated and unidentified SRM must exist. The recent development of high-throughput sequencing methods allows the phylogenetic identification of some of these uncultured SRM. In this study, we identified a novel putative SRM inhabiting hot spring microbial mats that is a member of the OPB56 clade (“Ca. Kapabacteria”) within the Bacteroidetes/Chlorobi superphylum. Partial genomes for this new organism were retrieved from metagenomes from three different hot springs in Yellowstone National Park, United States, and Japan. Supporting the prediction of a sulfate-reducing metabolism for this organism during period of anoxia, diel metatranscriptomic analyses indicate highest relative transcript levels in situ for all DSR-related genes at night. The presence of terminal oxidases, which are transcribed during the day, further suggests that these organisms might also perform aerobic respiration. The relative phylogenetic proximity to the sulfur-oxidizing, chlorophototrophic Chlorobi further raises new questions about the evolution of dissimilatory sulfur metabolism.
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Affiliation(s)
- Vera Thiel
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo, Japan.,Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
| | - Amaya M Garcia Costas
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States.,Department of Biology, Colorado State University-Pueblo, Pueblo, CO, United States
| | - Nathaniel W Fortney
- Department of Geoscience, University of Wisconsin-Madison, Madison, WI, United States
| | - Joval N Martinez
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo, Japan.,Department of Natural Sciences, University of St. La Salle, Bacolod, Philippines
| | - Marcus Tank
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo, Japan.,Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
| | - Eric E Roden
- Department of Geoscience, University of Wisconsin-Madison, Madison, WI, United States
| | - Eric S Boyd
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, United States
| | - David M Ward
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, United States
| | - Satoshi Hanada
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States.,Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
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118
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Smith HJ, Zelaya AJ, De León KB, Chakraborty R, Elias DA, Hazen TC, Arkin AP, Cunningham AB, Fields MW. Impact of hydrologic boundaries on microbial planktonic and biofilm communities in shallow terrestrial subsurface environments. FEMS Microbiol Ecol 2018; 94:5107865. [PMID: 30265315 PMCID: PMC6192502 DOI: 10.1093/femsec/fiy191] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 09/26/2018] [Indexed: 12/12/2022] Open
Abstract
Subsurface environments contain a large proportion of planetary microbial biomass and harbor diverse communities responsible for mediating biogeochemical cycles important to groundwater used by human society for consumption, irrigation, agriculture and industry. Within the saturated zone, capillary fringe and vadose zones, microorganisms can reside in two distinct phases (planktonic or biofilm), and significant differences in community composition, structure and activity between free-living and attached communities are commonly accepted. However, largely due to sampling constraints and the challenges of working with solid substrata, the contribution of each phase to subsurface processes is largely unresolved. Here, we synthesize current information on the diversity and activity of shallow freshwater subsurface habitats, discuss the challenges associated with sampling planktonic and biofilm communities across spatial, temporal and geological gradients, and discuss how biofilms may be constrained within shallow terrestrial subsurface aquifers. We suggest that merging traditional activity measurements and sequencing/-omics technologies with hydrological parameters important to sediment biofilm assembly and stability will help delineate key system parameters. Ultimately, integration will enhance our understanding of shallow subsurface ecophysiology in terms of bulk-flow through porous media and distinguish the respective activities of sessile microbial communities from more transient planktonic communities to ecosystem service and maintenance.
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Affiliation(s)
- H J Smith
- Center for Biofilm Engineering, Montana State University, Bozeman, MT
- ENIGMA (www.enigma.lbl.gov) Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS:977, Berkeley, CA 94720
| | - A J Zelaya
- Center for Biofilm Engineering, Montana State University, Bozeman, MT
- Department of Microbiology & Immunology, Montana State University, Bozeman, MT
- ENIGMA (www.enigma.lbl.gov) Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS:977, Berkeley, CA 94720
| | - K B De León
- Department of Biochemistry, University of Missouri, Columbia, MO
- ENIGMA (www.enigma.lbl.gov) Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS:977, Berkeley, CA 94720
| | - R Chakraborty
- Climate and Ecosystems Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA
- ENIGMA (www.enigma.lbl.gov) Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS:977, Berkeley, CA 94720
| | - D A Elias
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN
- ENIGMA (www.enigma.lbl.gov) Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS:977, Berkeley, CA 94720
| | - T C Hazen
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN
- ENIGMA (www.enigma.lbl.gov) Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS:977, Berkeley, CA 94720
| | - A P Arkin
- Department of Bioengineering, Lawrence Berkeley National Laboratory, Berkeley, CA
- ENIGMA (www.enigma.lbl.gov) Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS:977, Berkeley, CA 94720
| | - A B Cunningham
- Center for Biofilm Engineering, Montana State University, Bozeman, MT
- Department of Civil Engineering, Montana State University, Montana State University, Bozeman, MT
| | - M W Fields
- Center for Biofilm Engineering, Montana State University, Bozeman, MT
- Department of Microbiology & Immunology, Montana State University, Bozeman, MT
- ENIGMA (www.enigma.lbl.gov) Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS:977, Berkeley, CA 94720
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119
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Cheung MK, Wong CK, Chu KH, Kwan HS. Community Structure, Dynamics and Interactions of Bacteria, Archaea and Fungi in Subtropical Coastal Wetland Sediments. Sci Rep 2018; 8:14397. [PMID: 30258074 PMCID: PMC6158284 DOI: 10.1038/s41598-018-32529-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 09/06/2018] [Indexed: 01/04/2023] Open
Abstract
Bacteria, archaea and fungi play crucial roles in wetland biogeochemical processes. However, little is known about their community structure, dynamics and interactions in subtropical coastal wetlands. Here, we examined communities of the three kingdoms in mangrove and mudflat sediments of a subtropical coastal wetland using Ion Torrent amplicon sequencing and co-occurrence network analysis. Bacterial, archaeal and fungal communities comprised mainly of members from the phyla Proteobacteria and Bacteroidetes, Bathyarchaeota and Euryarchaeota, and Ascomycota, respectively. Species richness and Shannon diversity were highest in bacteria, followed by archaea and were lowest in fungi. Distinct spatiotemporal patterns were observed, with bacterial and fungal communities varying, to different extent, between wet and dry seasons and between mangrove and mudflat, and archaeal community remaining relatively stable between seasons and regions. Redundancy analysis revealed temperature as the major driver of the seasonal patterns of bacterial and fungal communities but also highlighted the importance of interkingdom biotic factors in shaping the community structure of all three kingdoms. Potential ecological interactions and putative keystone taxa were identified based on co-occurrence network analysis. These findings facilitate current understanding of the microbial ecology of subtropical coastal wetlands and provide a basis for better modelling of ecological processes in this important ecosystem.
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Affiliation(s)
- Man Kit Cheung
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Chong Kim Wong
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Ka Hou Chu
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Hoi Shan Kwan
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.
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120
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Mo Y, Zhang W, Yang J, Lin Y, Yu Z, Lin S. Biogeographic patterns of abundant and rare bacterioplankton in three subtropical bays resulting from selective and neutral processes. THE ISME JOURNAL 2018; 12:2198-2210. [PMID: 29880912 PMCID: PMC6092436 DOI: 10.1038/s41396-018-0153-6] [Citation(s) in RCA: 193] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 04/17/2018] [Accepted: 04/28/2018] [Indexed: 11/09/2022]
Abstract
Unraveling the relative importance of ecological processes regulating microbial community structure is a central goal in microbial ecology. Here, we used high-throughput sequencing to examine the relative contribution of selective and neutral processes in the assembly of abundant and rare subcommunities from three subtropical bays of China. We found that abundant and rare bacterial taxa were distinctly different in diversity, despite the similar biogeographic patterns and strong distance-decay relationships, but the dispersal of rare bacterial taxa was more limited than that of abundant taxa. Furthermore, the environmental (selective processes) and spatial (neutral processes) factors seemed to govern the assembly and biogeography of abundant and rare bacterial subcommunities, although both factors explained only a small fraction of variation within the rare subcommunity. More importantly, variation partitioning (based on adjusted R2 in redundancy analysis) showed that spatial factors exhibited a slightly greater influence on both abundant and rare subcommunities compared to environmental selection; however, the abundant subcommunity had a much stronger response to spatial factors (17.3% of pure variance was explained) than that shown by the rare bacteria (3.5%). These results demonstrate that environmental selection and neutral processes explained the similar biogeographic patterns of abundant and rare subcommunities, but a large proportion of unexplained variation in the rare taxa (91.1%) implies that more complex assembly mechanisms may exist to shape the rare bacterial assemblages in the three subtropical bays.
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Affiliation(s)
- Yuanyuan Mo
- State Key Laboratory of Marine Environmental Science, Marine Biodiversity and Global Change Research Center, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Wenjing Zhang
- State Key Laboratory of Marine Environmental Science, Marine Biodiversity and Global Change Research Center, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.
| | - Jun Yang
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China.
| | - Yuanshao Lin
- State Key Laboratory of Marine Environmental Science, Marine Biodiversity and Global Change Research Center, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Zheng Yu
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- Department of Chemical Engineering, University of Washington, Seattle, WA, USA
| | - Senjie Lin
- State Key Laboratory of Marine Environmental Science, Marine Biodiversity and Global Change Research Center, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Department of Marine Sciences, University of Connecticut, Groton, CT, USA
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121
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Jia X, Dini-Andreote F, Falcão Salles J. Community Assembly Processes of the Microbial Rare Biosphere. Trends Microbiol 2018; 26:738-747. [DOI: 10.1016/j.tim.2018.02.011] [Citation(s) in RCA: 137] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 02/12/2018] [Accepted: 02/22/2018] [Indexed: 01/19/2023]
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122
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Zehavi T, Probst M, Mizrahi I. Insights Into Culturomics of the Rumen Microbiome. Front Microbiol 2018; 9:1999. [PMID: 30210474 PMCID: PMC6123358 DOI: 10.3389/fmicb.2018.01999] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 08/08/2018] [Indexed: 01/17/2023] Open
Abstract
Cultivation of undescribed rumen microorganisms is one of the most important tasks in rumen microbiology. In this study, we aimed to discover the potential of culturomics for characterizing the rumen microbiome and for identifying factors, specifically sample dilution and media type, which affect microbial richness on agar plates. Our cultivation experiment captured 23% of all operational taxonomic units (OTUs) found in the rumen microbiome in this study. The use of different media increased the number of cultured OTUs by up to 40%. Sample dilution had the strongest effect on increasing richness on the plates, while abundance and phylogeny were the main factors determining cultivability of rumen microbes. Our findings from phylogenetic analysis of cultured OTUs on the lower branches of the phylogenetic tree suggest that multifactorial traits govern cultivability. Interestingly, most of our cultured OTUs belonged to the rare rumen biosphere. These cultured OTUs could not be detected in the rumen microbiome, even when we surveyed it across a 38 rumen microbiome samples. These findings add another unique dimension to the complexity of the rumen microbiome and suggest that a large number of different organisms can be cultured in a single cultivation effort.
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Affiliation(s)
- Tamar Zehavi
- Institute of Natural Sciences, Department of Life Sciences, Ben-Gurion University of the Negev, Beersheba, Israel
| | - Maraike Probst
- Institute of Natural Sciences, Department of Life Sciences, Ben-Gurion University of the Negev, Beersheba, Israel
| | - Itzhak Mizrahi
- Institute of Natural Sciences, Department of Life Sciences, Ben-Gurion University of the Negev, Beersheba, Israel
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123
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Understanding how microbiomes influence the systems they inhabit. Nat Microbiol 2018; 3:977-982. [DOI: 10.1038/s41564-018-0201-z] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 06/07/2018] [Accepted: 06/19/2018] [Indexed: 11/08/2022]
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124
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Bryukhanov AL, Vlasova MA, Malakhova TV, Perevalova AA, Pimenov NV. Phylogenetic Diversity of the Sulfur Cycle Bacteria in the Bottom Sediments of the Chersonesus Bay. Microbiology (Reading) 2018. [DOI: 10.1134/s0026261718030025] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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125
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Hausmann B, Pelikan C, Herbold CW, Köstlbacher S, Albertsen M, Eichorst SA, Glavina Del Rio T, Huemer M, Nielsen PH, Rattei T, Stingl U, Tringe SG, Trojan D, Wentrup C, Woebken D, Pester M, Loy A. Peatland Acidobacteria with a dissimilatory sulfur metabolism. THE ISME JOURNAL 2018; 12:1729-1742. [PMID: 29476143 PMCID: PMC6018796 DOI: 10.1038/s41396-018-0077-1] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 12/21/2017] [Accepted: 01/20/2018] [Indexed: 12/25/2022]
Abstract
Sulfur-cycling microorganisms impact organic matter decomposition in wetlands and consequently greenhouse gas emissions from these globally relevant environments. However, their identities and physiological properties are largely unknown. By applying a functional metagenomics approach to an acidic peatland, we recovered draft genomes of seven novel Acidobacteria species with the potential for dissimilatory sulfite (dsrAB, dsrC, dsrD, dsrN, dsrT, dsrMKJOP) or sulfate respiration (sat, aprBA, qmoABC plus dsr genes). Surprisingly, the genomes also encoded DsrL, which so far was only found in sulfur-oxidizing microorganisms. Metatranscriptome analysis demonstrated expression of acidobacterial sulfur-metabolism genes in native peat soil and their upregulation in diverse anoxic microcosms. This indicated an active sulfate respiration pathway, which, however, might also operate in reverse for dissimilatory sulfur oxidation or disproportionation as proposed for the sulfur-oxidizing Desulfurivibrio alkaliphilus. Acidobacteria that only harbored genes for sulfite reduction additionally encoded enzymes that liberate sulfite from organosulfonates, which suggested organic sulfur compounds as complementary energy sources. Further metabolic potentials included polysaccharide hydrolysis and sugar utilization, aerobic respiration, several fermentative capabilities, and hydrogen oxidation. Our findings extend both, the known physiological and genetic properties of Acidobacteria and the known taxonomic diversity of microorganisms with a DsrAB-based sulfur metabolism, and highlight new fundamental niches for facultative anaerobic Acidobacteria in wetlands based on exploitation of inorganic and organic sulfur molecules for energy conservation.
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Affiliation(s)
- Bela Hausmann
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Claus Pelikan
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Craig W Herbold
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Stephan Köstlbacher
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Mads Albertsen
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Stephanie A Eichorst
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | | | - Martin Huemer
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Per H Nielsen
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Thomas Rattei
- Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Ulrich Stingl
- Department for Microbiology and Cell Science, Fort Lauderdale Research and Education Center, UF/IFAS, University of Florida, Davie, FL, USA
| | - Susannah G Tringe
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Daniela Trojan
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Cecilia Wentrup
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Dagmar Woebken
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Michael Pester
- Department of Biology, University of Konstanz, Konstanz, Germany.
- Leibniz Institute DSMZ, Braunschweig, Germany.
| | - Alexander Loy
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
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126
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Vigneron A, Cruaud P, Alsop E, de Rezende JR, Head IM, Tsesmetzis N. Beyond the tip of the iceberg; a new view of the diversity of sulfite- and sulfate-reducing microorganisms. ISME JOURNAL 2018; 12:2096-2099. [PMID: 29805176 DOI: 10.1038/s41396-018-0155-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 02/09/2018] [Accepted: 03/09/2018] [Indexed: 11/09/2022]
Abstract
Sulfite-reducing and sulfate-reducing microorganisms (SRM) play important roles in anoxic environments, linking the sulfur and carbon cycles. With climate warming, the distribution of anoxic habitats conductive to dissimilatory SRM is expanding. Consequently, we hypothesize that novel SRM are likely to emerge from the rare biosphere triggered by environmental changes. Using the dsrB gene as a molecular marker of sulfite-reducers and sulfate-reducers, we analyzed the diversity, community composition, and abundance of SRM in 200 samples representing 14 different ecosystems, including marine and freshwater environments, oil reservoirs, and engineered infrastructure. Up to 167,397 species-level OTUs affiliated with 47 different families were identified. Up to 96% of these can be considered as "rare biosphere SRM". One third of the dsrB genes identified belonged to uncharacterized lineages. The dsrB sequences exhibited a strong pattern of selection in different ecosystems. These results expand our knowledge of the biodiversity and distribution of SRM, with implications for carbon and sulfur cycling in anoxic ecosystems.
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Affiliation(s)
- Adrien Vigneron
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle Upon Tyne, UK.,Shell International Exploration and Production Inc., Houston, TX, USA
| | - Perrine Cruaud
- INRA, UMR1062 CBGP, F-34988, Montferrier-sur-Lez, France
| | - Eric Alsop
- Shell International Exploration and Production Inc., Houston, TX, USA.,DOE Joint Genome Institute, Walnut Creek, CA, USA
| | | | - Ian M Head
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle Upon Tyne, UK.
| | - Nicolas Tsesmetzis
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle Upon Tyne, UK.,Shell International Exploration and Production Inc., Houston, TX, USA
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127
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Banerjee S, Schlaeppi K, van der Heijden MGA. Keystone taxa as drivers of microbiome structure and functioning. Nat Rev Microbiol 2018; 16:567-576. [DOI: 10.1038/s41579-018-0024-1] [Citation(s) in RCA: 839] [Impact Index Per Article: 139.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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128
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Benjamino J, Lincoln S, Srivastava R, Graf J. Low-abundant bacteria drive compositional changes in the gut microbiota after dietary alteration. MICROBIOME 2018; 6:86. [PMID: 29747692 PMCID: PMC5944116 DOI: 10.1186/s40168-018-0469-5] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 04/26/2018] [Indexed: 05/24/2023]
Abstract
BACKGROUND As the importance of beneficial bacteria is better recognized, understanding the dynamics of symbioses becomes increasingly crucial. In many gut symbioses, it is essential to understand whether changes in host diet play a role in the persistence of the bacterial gut community. In this study, termites were fed six dietary sources and the microbial community was monitored over a 49-day period using 16S rRNA gene sequencing. A deep backpropagation artificial neural network (ANN) was used to learn how the six different lignocellulose food sources affected the temporal composition of the hindgut microbiota of the termite as well as taxon-taxon and taxon-substrate interactions. RESULTS Shifts in the termite gut microbiota after diet change in each colony were observed using 16S rRNA gene sequencing and beta diversity analyses. The artificial neural network accurately predicted the relative abundances of taxa at random points in the temporal study and showed that low-abundant taxa maintain community driving correlations in the hindgut. CONCLUSIONS This combinatorial approach utilizing 16S rRNA gene sequencing and deep learning revealed that low-abundant bacteria that often do not belong to the core community are drivers of the termite hindgut bacterial community composition.
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Affiliation(s)
- Jacquelynn Benjamino
- Department of Molecular and Cell Biology, University of Connecticut, 91 N. Eagleville Road, U-3125, Storrs, CT, 06269, USA
| | - Stephen Lincoln
- Department of Chemical and Biomolecular Engineering, University of Connecticut, Storrs, CT, USA
| | - Ranjan Srivastava
- Department of Chemical and Biomolecular Engineering, University of Connecticut, Storrs, CT, USA
| | - Joerg Graf
- Department of Molecular and Cell Biology, University of Connecticut, 91 N. Eagleville Road, U-3125, Storrs, CT, 06269, USA.
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129
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Kaminsky R, Morales SE. Conditionally Rare Taxa Contribute but Do Not Account for Changes in Soil Prokaryotic Community Structure. Front Microbiol 2018; 9:809. [PMID: 29755437 PMCID: PMC5934496 DOI: 10.3389/fmicb.2018.00809] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 04/10/2018] [Indexed: 01/21/2023] Open
Abstract
The rare biosphere is predicted to aid in maintaining functional redundancy as well as contributing to community turnover across many environments. Recent developments have partially confirmed these hypotheses, while also giving new insights into dormancy and activity among rare communities. However, less attention has been paid to the rare biosphere in soils. This study provides insight into the rare biosphere’s contribution to soil microbial diversity through the study of 781 soil samples representing 24 edaphically diverse sites. Results show that Bray–Curtis dissimilarity for time-sensitive conditionally rare taxa (CRT) does not correlate with whole community dissimilarity, while dissimilarity for space-sensitive CRT only weakly correlate with whole community dissimilarity. This adds to current understanding of spatiotemporal filtering of rare taxa, showing that CRT do not account for community variance across tested soils, but are under the same selective pressure as the whole community.
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Affiliation(s)
- Rachel Kaminsky
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Sergio E Morales
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
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130
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Tao J, Meng D, Qin C, Liu X, Liang Y, Xiao Y, Liu Z, Gu Y, Li J, Yin H. Integrated network analysis reveals the importance of microbial interactions for maize growth. Appl Microbiol Biotechnol 2018. [PMID: 29532103 DOI: 10.1007/s00253-018-8837-4] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Microbes play a critical role in soil global biogeochemical circulation and microbe-microbe interactions have also evoked enormous interests in recent years. Utilization of green manures can stimulate microbial activity and affect microbial composition and diversity. However, few studies focus on the microbial interactions or detect the key functional members in communities. With the advances of metagenomic technologies, network analysis has been used as a powerful tool to detect robust interactions between microbial members. Here, random matrix theory-based network analysis was used to investigate the microbial networks in response to four different green manure fertilization regimes (Vicia villosa, common vetch, milk vetch, and radish) over two growth cycles from October 2012 to September 2014. The results showed that the topological properties of microbial networks were dramatically altered by green manure fertilization. Microbial network under milk vetch amendment showed substantially more intense complexity and interactions than other fertilization systems, indicating that milk vetch provided a favorable condition for microbial interactions and niche sharing. The shift of microbial interactions could be attributed to the changes in some major soil traits and the interactions might be correlated to plant growth and production. With the stimuli of green manures, positive interactions predominated the network eventually and the network complexity was in consistency with maize productivity, which suggested that the complex soil microbial networks might benefit to plants rather than simple ones, because complex networks would hold strong the ability to cope with environment changes or suppress soil-borne pathogen infection on plants. In addition, network analyses discerned some putative keystone taxa and seven of them had directly positive interactions with maize yield, which suggested their important roles in maintaining environmental functions and in improving plant growth.
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Affiliation(s)
- Jiemeng Tao
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,College of agronomy, Hunan Agricultural University, Changsha, China
| | - Delong Meng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Chong Qin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Yili Liang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Yunhua Xiao
- College of agronomy, Hunan Agricultural University, Changsha, China
| | - Zhenghua Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Yabing Gu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Juan Li
- College of agronomy, Hunan Agricultural University, Changsha, China.
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China. .,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China.
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131
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Meisner A, Jacquiod S, Snoek BL, Ten Hooven FC, van der Putten WH. Drought Legacy Effects on the Composition of Soil Fungal and Prokaryote Communities. Front Microbiol 2018; 9:294. [PMID: 29563897 PMCID: PMC5845876 DOI: 10.3389/fmicb.2018.00294] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 02/08/2018] [Indexed: 12/14/2022] Open
Abstract
It is increasingly acknowledged that climate change is influencing terrestrial ecosystems by increased drought and rainfall intensities. Soil microbes are key drivers of many processes in terrestrial systems and rely on water in soil pores to fulfill their life cycles and functions. However, little is known on how drought and rainfall fluctuations, which affect the composition and structure of microbial communities, persist once original moisture conditions have been restored. Here, we study how simulated short-term drying and re-wetting events shape the community composition of soil fungi and prokaryotes. In a mesocosm experiment, soil was exposed to an extreme drought, then re-wetted to optimal moisture (50% WHC, water holding capacity) or to saturation level (100% WHC). Composition, community structure and diversity of microbes were measured by sequencing ITS and 16S rRNA gene amplicons 3 weeks after original moisture content had been restored. Drying and extreme re-wetting decreased richness of microbial communities, but not evenness. Abundance changes were observed in only 8% of prokaryote OTUs, and 25% of fungal OTUs, whereas all other OTUs did not differ between drying and re-wetting treatments. Two specific legacy response groups (LRGs) were observed for both prokaryotes and fungi. OTUs belonging to the first LRG decreased in relative abundance in soil with a history of drought, whereas OTUs that increased in soil with a history of drought formed a second LRG. These microbial responses were spread among different phyla. Drought appeared to be more important for the microbial community composition than the following extreme re-wetting. 16S profiles were correlated with both inorganic N concentration and basal respiration and ITS profiles correlated with fungal biomass. We conclude that a drying and/or an extreme re-wetting history can persist in soil microbial communities via specific response groups composed of members with broad phylogenetic origins, with possible functional consequences on soil processes and plant species. As a large fraction of OTUs responding to drying and re-wetting belonged to the rare biosphere, our results suggest that low abundant microbial species are potentially important for ecosystem responses to extreme weather events.
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Affiliation(s)
- Annelein Meisner
- Microbial Ecology, Department of Biology, Lund University, Lund, Sweden.,Sections of Microbiology and Terrestrial Ecology, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands
| | | | - Basten L Snoek
- Department of Terrestrial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands.,Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, Netherlands.,Laboratory of Nematology, Wageningen University, Wageningen, Netherlands
| | - Freddy C Ten Hooven
- Department of Terrestrial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands
| | - Wim H van der Putten
- Department of Terrestrial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands.,Laboratory of Nematology, Wageningen University, Wageningen, Netherlands
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132
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Zhang S, Zhou Z, Li Y, Meng F. Deciphering the core fouling-causing microbiota in a membrane bioreactor: Low abundance but important roles. CHEMOSPHERE 2018; 195:108-118. [PMID: 29258007 DOI: 10.1016/j.chemosphere.2017.12.067] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 12/06/2017] [Accepted: 12/11/2017] [Indexed: 06/07/2023]
Abstract
Currently, membrane biofouling in membrane bioreactors (MBRs) is normally attributed to the occurrence of abundant bacterial species on membranes, whereas the roles of low-abundance bacteria have not been paid sufficient attention. In this study, the linear discriminant analysis (LDA) effect size (LEfSe) algorithm was used to identify active biomarkers, determining 67 different phylotypes among Bulk sludge, low-fouling Bio-cake (10 kPa), high-fouling Bio-cake (25 kPa) and Membrane pore in a membrane bioreactor with NaOCl backwash. Interestingly, a large proportion of the active biomarkers in bio-cake samples, such as Methylophilaceae, Burkholderiaceae, Paucibacter and Pseudoxanthomonas, did not fall within the abundant taxa (i.e., <0.05% relative abundance), indicating the preferential growth of these low-abundance bacteria on the membrane surface. Furthermore, the characterization of microbial interactions using a random matrix theory (RMT)-based network approach obtained a network consisting of 120 nodes and 228 edges. Specifically, network analysis showed the presence of an intense competition among bacterial species in the fouling-related communities, suggesting that negative interactions have an important effect on determining the microbial community structure. More importantly, the LEfSe algorithm and network analysis showed that most of the core species of the bio-cake, such as Burkholderiaceae, Bacillus and Rhodothermaceae, merely amounted to a very low relative abundance (<1%), suggesting their unrecognized and over-proportional ecological role in triggering the initial biofilm formation and subsequent biofilm maturation during MBR operation. Overall, this work should improve our understanding of the bacterial community structure on the fouled membranes in MBRs.
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Affiliation(s)
- Shaoqing Zhang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Zhongbo Zhou
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Yi Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, China
| | - Fangang Meng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, 510275, PR China.
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133
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Rezadehbashi M, Baldwin SA. Core Sulphate-Reducing Microorganisms in Metal-Removing Semi-Passive Biochemical Reactors and the Co-Occurrence of Methanogens. Microorganisms 2018; 6:microorganisms6010016. [PMID: 29473875 PMCID: PMC5874630 DOI: 10.3390/microorganisms6010016] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 02/14/2018] [Accepted: 02/17/2018] [Indexed: 11/25/2022] Open
Abstract
Biochemical reactors (BCRs) based on the stimulation of sulphate-reducing microorganisms (SRM) are emerging semi-passive remediation technologies for treatment of mine-influenced water. Their successful removal of metals and sulphate has been proven at the pilot-scale, but little is known about the types of SRM that grow in these systems and whether they are diverse or restricted to particular phylogenetic or taxonomic groups. A phylogenetic study of four established pilot-scale BCRs on three different mine sites compared the diversity of SRM growing in them. The mine sites were geographically distant from each other, nevertheless the BCRs selected for similar SRM types. Clostridia SRM related to Desulfosporosinus spp. known to be tolerant to high concentrations of copper were members of the core microbial community. Members of the SRM family Desulfobacteraceae were dominant, particularly those related to Desulfatirhabdium butyrativorans. Methanogens were dominant archaea and possibly were present at higher relative abundances than SRM in some BCRs. Both hydrogenotrophic and acetoclastic types were present. There were no strong negative or positive co-occurrence correlations of methanogen and SRM taxa. Knowing which SRM inhabit successfully operating BCRs allows practitioners to target these phylogenetic groups when selecting inoculum for future operations.
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Affiliation(s)
- Maryam Rezadehbashi
- Chemical and Biological Engineering, University of British Columbia, 2360 East Mall, Vancouver, BC V6T 1Z3, Canada.
| | - Susan A Baldwin
- Chemical and Biological Engineering, University of British Columbia, 2360 East Mall, Vancouver, BC V6T 1Z3, Canada.
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134
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Yang S, Winkel M, Wagner D, Liebner S. Community structure of rare methanogenic archaea: insight from a single functional group. FEMS Microbiol Ecol 2018; 93:4331631. [PMID: 29029047 PMCID: PMC5812523 DOI: 10.1093/femsec/fix126] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 09/29/2017] [Indexed: 11/24/2022] Open
Abstract
The rare biosphere, the low abundant microbial populations, is suggested to be a conserved way of microbial life. Here we conducted a molecular survey of rare methanogenic archaea in the environment targeting the mcrA gene in order to test if general concepts associated with the structure of the rare bacterial biosphere also apply to single functional groups. Similar to what is known about rare bacterial communities, the contribution of rare methanogens to the alpha diversity is much larger than to Bray-Curtis measures. Moreover, a similar core group of methanogens harbored by the abundant and rare communities suggests similar sources and environmental controls of both groups. Among the communities of different levels of rarity, the conditionally rare methanogenic taxa largely account for the overall community dynamics of the rare biosphere and likely enter the dominant community under favorable environmental conditions. In addition, we observed a positive correlation between the alpha diversity and the production of methane when the rare taxa were taken into account. This supports the concept that increasing microbial biodiversity enhances ecological function. The composition and environmental associations of the rare methanogenic biosphere allow us to conclude that rarity is a conserved way also for single functional groups.
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Affiliation(s)
- Sizhong Yang
- GFZ German Research Center for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, 14473 Potsdam, Germany.,State Key Laboratory of Frozen Soil Engineering, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, 730000 Lanzhou, China
| | - Matthias Winkel
- GFZ German Research Center for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, 14473 Potsdam, Germany
| | - Dirk Wagner
- GFZ German Research Center for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, 14473 Potsdam, Germany
| | - Susanne Liebner
- GFZ German Research Center for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, 14473 Potsdam, Germany
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135
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Hausmann B, Pjevac P, Schreck K, Herbold CW, Daims H, Wagner M, Loy A. Draft Genome Sequence of Telmatospirillum siberiense 26-4b1, an Acidotolerant Peatland Alphaproteobacterium Potentially Involved in Sulfur Cycling. GENOME ANNOUNCEMENTS 2018; 6:e01524-17. [PMID: 29371357 PMCID: PMC5786683 DOI: 10.1128/genomea.01524-17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 12/21/2017] [Indexed: 11/20/2022]
Abstract
The facultative anaerobic chemoorganoheterotrophic alphaproteobacterium Telmatospirillum siberiense 26-4b1 was isolated from a Siberian peatland. We report here a 6.20-Mbp near-complete high-quality draft genome sequence of T. siberiense that reveals expected and novel metabolic potential for the genus Telmatospirillum, including genes for sulfur oxidation.
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Affiliation(s)
- Bela Hausmann
- Research Network Chemistry meets Microbiology, Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Petra Pjevac
- Research Network Chemistry meets Microbiology, Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Katharina Schreck
- Research Network Chemistry meets Microbiology, Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Craig W Herbold
- Research Network Chemistry meets Microbiology, Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Holger Daims
- Research Network Chemistry meets Microbiology, Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Michael Wagner
- Research Network Chemistry meets Microbiology, Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Alexander Loy
- Research Network Chemistry meets Microbiology, Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
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136
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Winkel M, Mitzscherling J, Overduin PP, Horn F, Winterfeld M, Rijkers R, Grigoriev MN, Knoblauch C, Mangelsdorf K, Wagner D, Liebner S. Anaerobic methanotrophic communities thrive in deep submarine permafrost. Sci Rep 2018; 8:1291. [PMID: 29358665 PMCID: PMC5778128 DOI: 10.1038/s41598-018-19505-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 12/22/2017] [Indexed: 11/09/2022] Open
Abstract
Thawing submarine permafrost is a source of methane to the subsurface biosphere. Methane oxidation in submarine permafrost sediments has been proposed, but the responsible microorganisms remain uncharacterized. We analyzed archaeal communities and identified distinct anaerobic methanotrophic assemblages of marine and terrestrial origin (ANME-2a/b, ANME-2d) both in frozen and completely thawed submarine permafrost sediments. Besides archaea potentially involved in anaerobic oxidation of methane (AOM) we found a large diversity of archaea mainly belonging to Bathyarchaeota, Thaumarchaeota, and Euryarchaeota. Methane concentrations and δ13C-methane signatures distinguish horizons of potential AOM coupled either to sulfate reduction in a sulfate-methane transition zone (SMTZ) or to the reduction of other electron acceptors, such as iron, manganese or nitrate. Analysis of functional marker genes (mcrA) and fluorescence in situ hybridization (FISH) corroborate potential activity of AOM communities in submarine permafrost sediments at low temperatures. Modeled potential AOM consumes 72-100% of submarine permafrost methane and up to 1.2 Tg of carbon per year for the total expected area of submarine permafrost. This is comparable with AOM habitats such as cold seeps. We thus propose that AOM is active where submarine permafrost thaws, which should be included in global methane budgets.
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Affiliation(s)
- Matthias Winkel
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, 14473, Potsdam, Germany.
| | - Julia Mitzscherling
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, 14473, Potsdam, Germany
| | - Pier P Overduin
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Periglacial Research, 14473, Potsdam, Germany
| | - Fabian Horn
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, 14473, Potsdam, Germany
| | - Maria Winterfeld
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Marine Geochemistry, 27570, Bremerhaven, Germany
| | - Ruud Rijkers
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, 14473, Potsdam, Germany
| | | | | | - Kai Mangelsdorf
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 3.2 Organic Geochemistry, 14473, Potsdam, Germany
| | - Dirk Wagner
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, 14473, Potsdam, Germany
| | - Susanne Liebner
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, 14473, Potsdam, Germany
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137
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Diversity of Sulfur-Oxidizing and Sulfur-Reducing Microbes in Diverse Ecosystems. ADVANCES IN SOIL MICROBIOLOGY: RECENT TRENDS AND FUTURE PROSPECTS 2018. [DOI: 10.1007/978-981-10-6178-3_4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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138
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Tucker SJ, McManus GB, Katz LA, Grattepanche JD. Distribution of Abundant and Active Planktonic Ciliates in Coastal and Slope Waters Off New England. Front Microbiol 2017; 8:2178. [PMID: 29250036 PMCID: PMC5715329 DOI: 10.3389/fmicb.2017.02178] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 10/23/2017] [Indexed: 11/18/2022] Open
Abstract
Despite their important role of linking microbial and classic marine food webs, data on biogeographical patterns of microbial eukaryotic grazers are limited, and even fewer studies have used molecular tools to assess active (i.e., those expressing genes) community members. Marine ciliate diversity is believed to be greatest at the chlorophyll maximum, where there is an abundance of autotrophic prey, and is often assumed to decline with depth. Here, we assess the abundant (DNA) and active (RNA) marine ciliate communities throughout the water column at two stations off the New England coast (Northwest Atlantic)—a coastal station 43 km from shore (40 m depth) and a slope station 135 km off shore (1,000 m). We analyze ciliate communities using a DNA fingerprinting technique, Denaturing Gradient Gel Electrophoresis (DGGE), which captures patterns of abundant community members. We compare estimates of ciliate communities from SSU-rDNA (abundant) and SSU-rRNA (active) and find complex patterns throughout the water column, including many active lineages below the photic zone. Our analyses reveal (1) a number of widely-distributed taxa that are both abundant and active; (2) considerable heterogeneity in patterns of presence/absence of taxa in offshore samples taken 50 m apart throughout the water column; and (3) three distinct ciliate assemblages based on position from shore and depth. Analysis of active (RNA) taxa uncovers biodiversity hidden to traditional DNA-based approaches (e.g., clone library, rDNA amplicon studies).
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Affiliation(s)
- Sarah J Tucker
- Department of Biological Sciences, Smith College, Northampton, MA, United States
| | - George B McManus
- Department of Marine Sciences, University of Connecticut, Groton, CT, United States
| | - Laura A Katz
- Department of Biological Sciences, Smith College, Northampton, MA, United States.,Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst, MA, United States
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139
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Van Goethem MW, Makhalanyane TP, Cowan DA, Valverde A. Cyanobacteria and Alphaproteobacteria May Facilitate Cooperative Interactions in Niche Communities. Front Microbiol 2017; 8:2099. [PMID: 29118751 PMCID: PMC5660985 DOI: 10.3389/fmicb.2017.02099] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 10/13/2017] [Indexed: 01/04/2023] Open
Abstract
Hypoliths, microbial assemblages found below translucent rocks, provide important ecosystem services in deserts. While several studies have assessed microbial diversity of hot desert hypoliths and whether these communities are metabolically active, the interactions among taxa remain unclear. Here, we assessed the structure, diversity, and co-occurrence patterns of hypolithic communities from the hyperarid Namib Desert by comparing total (DNA) and potentially active (RNA) communities. The potentially active and total hypolithic communities differed in their composition and diversity, with significantly higher levels of Cyanobacteria and Alphaproteobacteria in potentially active hypoliths. Several phyla known to be abundant in total hypolithic communities were metabolically inactive, indicating that some hypolithic taxa may be dormant or dead. The potentially active hypolith network was highly modular in structure with almost exclusively positive co-occurrences (>95% of the total) between taxa. Members of the Cyanobacteria and Alphaproteobacteria were identified as potential keystone taxa, and exhibited numerous positive co-occurrences with other microbes, suggesting that these groups might have important roles in maintaining network topological structure despite their low abundance.
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Affiliation(s)
- Marc W Van Goethem
- Centre for Microbial Ecology and Genomics, Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - Thulani P Makhalanyane
- Centre for Microbial Ecology and Genomics, Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics, Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - Angel Valverde
- Centre for Microbial Ecology and Genomics, Department of Genetics, University of Pretoria, Pretoria, South Africa
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140
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Antwis RE, Griffiths SM, Harrison XA, Aranega-Bou P, Arce A, Bettridge AS, Brailsford FL, de Menezes A, Devaynes A, Forbes KM, Fry EL, Goodhead I, Haskell E, Heys C, James C, Johnston SR, Lewis GR, Lewis Z, Macey MC, McCarthy A, McDonald JE, Mejia-Florez NL, O'Brien D, Orland C, Pautasso M, Reid WDK, Robinson HA, Wilson K, Sutherland WJ. Fifty important research questions in microbial ecology. FEMS Microbiol Ecol 2017; 93:3098413. [PMID: 28379446 DOI: 10.1093/femsec/fix044] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 03/31/2017] [Indexed: 11/13/2022] Open
Abstract
Microbial ecology provides insights into the ecological and evolutionary dynamics of microbial communities underpinning every ecosystem on Earth. Microbial communities can now be investigated in unprecedented detail, although there is still a wealth of open questions to be tackled. Here we identify 50 research questions of fundamental importance to the science or application of microbial ecology, with the intention of summarising the field and bringing focus to new research avenues. Questions are categorised into seven themes: host-microbiome interactions; health and infectious diseases; human health and food security; microbial ecology in a changing world; environmental processes; functional diversity; and evolutionary processes. Many questions recognise that microbes provide an extraordinary array of functional diversity that can be harnessed to solve real-world problems. Our limited knowledge of spatial and temporal variation in microbial diversity and function is also reflected, as is the need to integrate micro- and macro-ecological concepts, and knowledge derived from studies with humans and other diverse organisms. Although not exhaustive, the questions presented are intended to stimulate discussion and provide focus for researchers, funders and policy makers, informing the future research agenda in microbial ecology.
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Affiliation(s)
- Rachael E Antwis
- School of Environment and Life Sciences, University of Salford, The Crescent, Salford M5 4WT, UK
| | - Sarah M Griffiths
- School of Science and the Environment, Manchester Metropolitan University, Manchester, Greater Manchester M1 5GD, UK
| | - Xavier A Harrison
- Institute of Zoology, Zoological Society of London, London, London NW1 4RY, UK
| | - Paz Aranega-Bou
- School of Environment and Life Sciences, University of Salford, The Crescent, Salford M5 4WT, UK
| | - Andres Arce
- Silwood Park, Faculty of Natural Sciences, Imperial College London, London, London SW7 2AZ, UK
| | - Aimee S Bettridge
- School of Biosciences, Cardiff University, Cardiff, South Glamorgan CF10 3XQ, UK
| | - Francesca L Brailsford
- School of Environment, Natural Resources and Geography, Bangor University, Bangor, Gwynedd LL57 2DG, UK
| | - Alexandre de Menezes
- School of Environment and Life Sciences, University of Salford, The Crescent, Salford M5 4WT, UK
| | - Andrew Devaynes
- Biosciences, Edge Hill University, Ormskirk, Lancashire L39 4QP, UK
| | - Kristian M Forbes
- Department of Virology, University of Helsinki, Helsinki 00014, Finland
| | - Ellen L Fry
- School of Earth and Environmental Sciences, Faculty of Science and Engineering, University of Manchester, Manchester M13 9PT, UK
| | - Ian Goodhead
- School of Environment and Life Sciences, University of Salford, The Crescent, Salford M5 4WT, UK
| | - Erin Haskell
- Department of Biology, University of York, York, North Yorkshire YO10 5DD, UK
| | - Chloe Heys
- Institute of Integrative Biology/School of Life Sciences, University of Liverpool, Liverpool, Merseyside L69 3BX, UK
| | - Chloe James
- School of Environment and Life Sciences, University of Salford, The Crescent, Salford M5 4WT, UK
| | - Sarah R Johnston
- School of Biosciences, Cardiff University, Cardiff, South Glamorgan CF10 3XQ, UK
| | - Gillian R Lewis
- Biosciences, Edge Hill University, Ormskirk, Lancashire L39 4QP, UK
| | - Zenobia Lewis
- Institute of Integrative Biology/School of Life Sciences, University of Liverpool, Liverpool, Merseyside L69 3BX, UK
| | - Michael C Macey
- School of Environmental Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - Alan McCarthy
- Institute of Integrative Biology/School of Life Sciences, University of Liverpool, Liverpool, Merseyside L69 3BX, UK
| | - James E McDonald
- School of Biological Sciences, Bangor University, Bangor, Gwynedd LL57 2DG, UK
| | | | | | - Chloé Orland
- Department of Plant Sciences, University of Cambridge, Cambridge, Cambridgeshire CB2 1TN, UK
| | - Marco Pautasso
- Animal and Plant Health Unit, European Food Safety Authority, Parma 43126, Italy
| | - William D K Reid
- School of Biology, Newcastle University, Newcastle upon Tyne, Tyne and Wear NE1 7RU, UK
| | - Heather A Robinson
- School of Earth and Environmental Sciences, Faculty of Science and Engineering, University of Manchester, Manchester M13 9PT, UK
| | - Kenneth Wilson
- Lancaster Environment Centre, Lancaster University, Lancaster, Lancashire LA1 4YW, UK
| | - William J Sutherland
- Conservation Science Group, Department of Zoology, University of Cambridge, Cambridge, Cambridgeshire CB2 1TN, UK
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141
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Introduced ascidians harbor highly diverse and host-specific symbiotic microbial assemblages. Sci Rep 2017; 7:11033. [PMID: 28887506 PMCID: PMC5591302 DOI: 10.1038/s41598-017-11441-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 08/22/2017] [Indexed: 11/24/2022] Open
Abstract
Many ascidian species have experienced worldwide introductions, exhibiting remarkable success in crossing geographic borders and adapting to local environmental conditions. To investigate the potential role of microbial symbionts in these introductions, we examined the microbial communities of three ascidian species common in North Carolina harbors. Replicate samples of the globally introduced species Distaplia bermudensis, Polyandrocarpa anguinea, and P. zorritensis (n = 5), and ambient seawater (n = 4), were collected in Wrightsville Beach, NC. Microbial communities were characterized by next-generation (Illumina) sequencing of partial (V4) 16S rRNA gene sequences. Ascidians hosted diverse symbiont communities, consisting of 5,696 unique microbial OTUs (at 97% sequenced identity) from 44 bacterial and three archaeal phyla. Permutational multivariate analyses of variance revealed clear differentiation of ascidian symbionts compared to seawater bacterioplankton, and distinct microbial communities inhabiting each ascidian species. 103 universal core OTUs (present in all ascidian replicates) were identified, including taxa previously described in marine invertebrate microbiomes with possible links to ammonia-oxidization, denitrification, pathogenesis, and heavy-metal processing. These results suggest ascidian microbial symbionts exhibit a high degree of host-specificity, forming intimate associations that may contribute to host adaptation to new environments via expanded tolerance thresholds and enhanced holobiont function.
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142
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Singer E, Wagner M, Woyke T. Capturing the genetic makeup of the active microbiome in situ. THE ISME JOURNAL 2017; 11:1949-1963. [PMID: 28574490 PMCID: PMC5563950 DOI: 10.1038/ismej.2017.59] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 03/02/2017] [Accepted: 03/10/2017] [Indexed: 12/21/2022]
Abstract
More than any other technology, nucleic acid sequencing has enabled microbial ecology studies to be complemented with the data volumes necessary to capture the extent of microbial diversity and dynamics in a wide range of environments. In order to truly understand and predict environmental processes, however, the distinction between active, inactive and dead microbial cells is critical. Also, experimental designs need to be sensitive toward varying population complexity and activity, and temporal as well as spatial scales of process rates. There are a number of approaches, including single-cell techniques, which were designed to study in situ microbial activity and that have been successively coupled to nucleic acid sequencing. The exciting new discoveries regarding in situ microbial activity provide evidence that future microbial ecology studies will indispensably rely on techniques that specifically capture members of the microbiome active in the environment. Herein, we review those currently used activity-based approaches that can be directly linked to shotgun nucleic acid sequencing, evaluate their relevance to ecology studies, and discuss future directions.
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Affiliation(s)
- Esther Singer
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Michael Wagner
- University of Vienna, Department of Microbial Ecology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Tanja Woyke
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
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143
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Jiao S, Luo Y, Lu M, Xiao X, Lin Y, Chen W, Wei G. Distinct succession patterns of abundant and rare bacteria in temporal microcosms with pollutants. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2017; 225:497-505. [PMID: 28336094 DOI: 10.1016/j.envpol.2017.03.015] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 02/16/2017] [Accepted: 03/07/2017] [Indexed: 05/20/2023]
Abstract
Elucidating the driving forces behind the temporal dynamics of abundant and rare microbes is essential for understanding the assembly and succession of microbial communities. Here, we explored the successional trajectories and mechanisms of abundant and rare bacteria via soil-enrichment subcultures in response to various pollutants (phenanthrene, n-octadecane, and CdCl2) using time-series Illumina sequencing datasets. The results reveal different successional patterns of abundant and rare sub-communities in eighty pollutant-degrading consortia and two original soil samples. A temporal decrease in α-diversity and high turnover rate for β-diversity indicate that deterministic processes are the main drivers of the succession of the abundant sub-community; however, the high cumulative species richness indicates that stochastic processes drive the succession of the rare sub-community. A functional prediction showed that abundant bacteria contribute primary functions to the pollutant-degrading consortia, such as amino acid metabolism, cellular responses to stress, and hydrocarbon degradation. Meanwhile, rare bacteria contribute a substantial fraction of auxiliary functions, such as carbohydrate-active enzymes, fermentation, and homoacetogenesis, which indicates their roles as a source of functional diversity. Our study suggests that the temporal succession of microbes in polluted microcosms is mainly associated with abundant bacteria rather than the high proportion of rare taxa. The major forces (i.e., stochastic or deterministic processes) driving microbial succession could be dependent on the low- or high-abundance community members in temporal microcosms with pollutants.
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Affiliation(s)
- Shuo Jiao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Yantao Luo
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Mingmei Lu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Xiao Xiao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Yanbing Lin
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Weimin Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China.
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China.
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144
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Dawson W, Hör J, Egert M, van Kleunen M, Pester M. A Small Number of Low-abundance Bacteria Dominate Plant Species-specific Responses during Rhizosphere Colonization. Front Microbiol 2017; 8:975. [PMID: 28611765 PMCID: PMC5447024 DOI: 10.3389/fmicb.2017.00975] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 05/15/2017] [Indexed: 12/31/2022] Open
Abstract
Plant growth can be affected by soil bacteria. In turn, plants are known to influence soil bacteria through rhizodeposits and changes in abiotic conditions. We aimed to quantify the phylotype richness and relative abundance of rhizosphere bacteria that are actually influenced in a plant species-specific manner and to determine the role of the disproportionately large diversity of low-abundance bacteria belonging to the rare biosphere (<0.1 relative abundance) in this process. In addition, we aimed to determine whether plant phylogeny has an influence on the plant species-specific rhizosphere bacterial community. For this purpose, 19 herbaceous plant species from five different plant orders were grown in a common soil substrate. Bacterial communities in the initial soil substrate and the established rhizosphere soils were compared by 16S rRNA gene amplicon sequencing. Only a small number of bacterial operational taxonomic units (OTUs, 97% sequence identity) responded either positively (ca. 1%) or negatively (ca. 1%) to a specific plant species. On average, 91% of plant-specific positive response OTUs comprised bacteria belonging to the rare biosphere, highlighting that low-abundance populations are metabolically active in the rhizosphere. In addition, low-abundance OTUs were in terms of their summed relative abundance major drivers of the bacterial phyla composition across the rhizosphere of all tested plant species. However, no effect of plant phylogeny could be observed on the established rhizosphere bacterial communities, neither when considering differences in the overall established rhizosphere communities nor when considering plant species-specific responders only. Our study provides a quantitative assessment of the effect of plants on their rhizosphere bacteria across multiple plant orders. Plant species-specific effects on soil bacterial communities involved only 18–111 bacterial OTUs out of several 1000s; this minority may potentially impact plant growth in plant–bacteria interactions.
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Affiliation(s)
- Wayne Dawson
- Department of Biosciences, Durham UniversityDurham, United Kingdom.,Department of Biology, University of KonstanzKonstanz, Germany
| | - Jens Hör
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Furtwangen UniversityVillingen-Schwenningen, Germany
| | - Markus Egert
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Furtwangen UniversityVillingen-Schwenningen, Germany
| | | | - Michael Pester
- Department of Biology, University of KonstanzKonstanz, Germany
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145
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Low abundant soil bacteria can be metabolically versatile and fast growing. Ecology 2017; 98:555-564. [DOI: 10.1002/ecy.1670] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 11/09/2016] [Accepted: 11/17/2016] [Indexed: 11/07/2022]
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146
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Distinct Anaerobic Bacterial Consumers of Cellobiose-Derived Carbon in Boreal Fens with Different CO2/CH4 Production Ratios. Appl Environ Microbiol 2017; 83:AEM.02533-16. [PMID: 27913414 DOI: 10.1128/aem.02533-16] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 11/28/2016] [Indexed: 11/20/2022] Open
Abstract
Northern peatlands in general have high methane (CH4) emissions, but individual peatlands show considerable variation as CH4 sources. Particularly in nutrient-poor peatlands, CH4 production can be low and exceeded by carbon dioxide (CO2) production from unresolved anaerobic processes. To clarify the role anaerobic bacterial degraders play in this variation, we compared consumers of cellobiose-derived carbon in two fens differing in nutrient status and the ratio of CO2 to CH4 produced. After [13C]cellobiose amendment, the mesotrophic fen produced equal amounts of CH4 and CO2 The oligotrophic fen had lower CH4 production but produced 3 to 59 times more CO2 than CH4 RNA stable-isotope probing revealed that in the mesotrophic fen with higher CH4 production, cellobiose-derived carbon was mainly assimilated by various recognized fermenters of Firmicutes and by Proteobacteria The oligotrophic peat with excess CO2 production revealed a wider variety of cellobiose-C consumers, including Firmicutes and Proteobacteria, but also more unconventional degraders, such as Telmatobacter-related Acidobacteria and subphylum 3 of Verrucomicrobia Prominent and potentially fermentative Planctomycetes and Chloroflexi did not appear to process cellobiose-C. Our results show that anaerobic degradation resulting in different levels of CH4 production can involve distinct sets of bacterial degraders. By distinguishing cellobiose degraders from the total community, this study contributes to defining anaerobic bacteria that process cellulose-derived carbon in peat. Several of the identified degraders, particularly fermenters and potential Fe(III) or humic substance reducers in the oligotrophic peat, represent promising candidates for resolving the origin of excess CO2 production in peatlands. IMPORTANCE Peatlands are major sources of the greenhouse gas methane (CH4), yet in many peatlands, CO2 production from unresolved anaerobic processes exceeds CH4 production. Anaerobic degradation produces the precursors of CH4 production but also represents competing processes. We show that anaerobic degradation leading to high or low CH4 production involved distinct sets of bacteria. Well-known fermenters dominated in a peatland with high CH4 production, while novel and unconventional degraders could be identified in a site where CO2 production greatly exceeds CH4 production. Our results help identify and assign functions to uncharacterized bacteria that promote or inhibit CH4 production and reveal bacteria potentially producing the excess CO2 in acidic peat. This study contributes to understanding the microbiological basis for different levels of CH4 emission from peatlands.
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147
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Jiao S, Zhang Z, Yang F, Lin Y, Chen W, Wei G. Temporal dynamics of microbial communities in microcosms in response to pollutants. Mol Ecol 2017; 26:923-936. [PMID: 28012222 DOI: 10.1111/mec.13978] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 12/08/2016] [Indexed: 01/18/2023]
Abstract
Elucidating the mechanisms underlying microbial succession is a major goal of microbial ecology research. Given the increasing human pressure on the environment and natural resources, responses to the repeated introduction of organic and inorganic pollutants are of particular interest. To investigate the temporal dynamics of microbial communities in response to pollutants, we analysed the microbial community structure in batch microcosms that were inoculated with soil bacteria following exposure to individual or combined pollutants (phenanthrene, n-octadecane, phenanthrene + n-octadecane and phenanthrene + n-octadecane + CdCl2 ). Subculturing was performed at 10-day intervals, followed by high-throughput sequencing of 16S rRNA genes. The dynamics of microbial communities in response to different pollutants alone and in combination displayed similar patterns during enrichment. Specifically, the repression and induction of microbial taxa were dominant, and the fluctuation was not significant. The rate of appearance for new taxa and the temporal turnover within microbial communities were higher than the rates reported in other studies of microbial communities in air, water and soil samples. In addition, conditionally rare taxa that were specific to the treatments exhibited higher betweenness centrality values in the co-occurrence network, indicating a strong influence on other interactions in the community. These results suggest that the repeated introduction of pollutants could accelerate microbial succession in microcosms, resulting in the rapid re-equilibration of microbial communities.
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Affiliation(s)
- Shuo Jiao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Zhengqing Zhang
- Laboratory of Forestry Pests Biological Control, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Fan Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yanbing Lin
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Weimin Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
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148
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Wu W, Logares R, Huang B, Hsieh CH. Abundant and rare picoeukaryotic sub-communities present contrasting patterns in the epipelagic waters of marginal seas in the northwestern Pacific Ocean. Environ Microbiol 2017; 19:287-300. [PMID: 27871146 DOI: 10.1111/1462-2920.13606] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 11/02/2016] [Accepted: 11/08/2016] [Indexed: 01/22/2023]
Abstract
In this work, they compared patterns of abundant and rare picoeukaryotic sub-communities in the epipelagic waters (surface and 40-75 m depth subsurface layers) of the East and South China Seas across seasons via 454 pyrosequencing of the V4 region of 18S rDNA. They also examined the relative effects of environmental filtering, dispersal limitations and seasonality on community assembly. Their results indicated that (i) in the surface layer, abundant taxa are primarily influenced by dispersal limitations and rare taxa are primarily influenced by environmental filtering, whereas (ii) in the subsurface layer, both abundant and rare sub-communities are only weakly influenced by environmental filtering but are strongly influenced by dispersal limitations. Moreover, (iii) abundant taxa exhibit stronger temporal variability than rare taxa. They also found that abundant and rare sub-communities display similar spatial richness patterns that are negatively correlated with latitude and chlorophyll a and positively correlated with temperature. In summary, environmental filtering and dispersal limitations have different effects on abundant and rare picoeukaryotic sub-communities in different layers. Thus, depth appears as an essential variable that governs the structuring patterns of picoeukaryotic communities in the oceans and should be thoroughly considered to develop a more comprehensive understanding of oceanic microbial assemblages.
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Affiliation(s)
- Wenxue Wu
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China.,Key Laboratory of Coastal and Wetland Ecosystems, Xiamen University, Xiamen, China.,Institute of Oceanography, National Taiwan University, Taipei, Taiwan
| | - Ramiro Logares
- Institut de Ciències del Mar (ICM), CSIC, Barcelona, Catalonia, Spain
| | - Bangqin Huang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China.,Key Laboratory of Coastal and Wetland Ecosystems, Xiamen University, Xiamen, China
| | - Chih-Hao Hsieh
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan.,Institute of Ecology and Evolutionary Biology, Department of Life Science, National Taiwan University, Taipei, Taiwan.,Research Center for Environmental Changes, Taipei, Taiwan.,National Center for Theoretical Sciences, Taipei, Taiwan
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Where less may be more: how the rare biosphere pulls ecosystems strings. ISME JOURNAL 2017; 11:853-862. [PMID: 28072420 PMCID: PMC5364357 DOI: 10.1038/ismej.2016.174] [Citation(s) in RCA: 581] [Impact Index Per Article: 83.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 11/06/2016] [Accepted: 11/12/2016] [Indexed: 02/05/2023]
Abstract
Rare species are increasingly recognized as crucial, yet vulnerable components of Earth's ecosystems. This is also true for microbial communities, which are typically composed of a high number of relatively rare species. Recent studies have demonstrated that rare species can have an over-proportional role in biogeochemical cycles and may be a hidden driver of microbiome function. In this review, we provide an ecological overview of the rare microbial biosphere, including causes of rarity and the impacts of rare species on ecosystem functioning. We discuss how rare species can have a preponderant role for local biodiversity and species turnover with rarity potentially bound to phylogenetically conserved features. Rare microbes may therefore be overlooked keystone species regulating the functioning of host-associated, terrestrial and aquatic environments. We conclude this review with recommendations to guide scientists interested in investigating this rapidly emerging research area.
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Yu Z, He Z, Tao X, Zhou J, Yang Y, Zhao M, Zhang X, Zheng Z, Yuan T, Liu P, Chen Y, Nolan V, Li X. The shifts of sediment microbial community phylogenetic and functional structures during chromium (VI) reduction. ECOTOXICOLOGY (LONDON, ENGLAND) 2016; 25:1759-1770. [PMID: 27637513 DOI: 10.1007/s10646-016-1719-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 08/29/2016] [Indexed: 05/13/2023]
Abstract
The Lanzhou reach of the Yellow River, located at the upstream of Lanzhou, has been contaminated by heavy metals and polycyclic aromatic hydrocarbons over a long-time. We hypothesized that indigenous microbial communities would remediate those contaminants and some unique populations could play an important role in this process. In this study, we investigated the sediment microbial community structure and function from the Lanzhou reach. Sediment samples were collected from two nearby sites (site A and site B) in the Lanzhou reach along the Yellow River. Sediment geochemical property data showed that site A sediment samples contained significantly (p < 0.05) higher heavy metals than site B, such as chromium (Cr), manganese (Mn), and copper (Cu). Both site A and B samples were incubated with or without hexavalent chromium (Cr (VI)) for 30 days in the laboratory, and Cr (VI) reduction was only observed in site A sediment samples. After incubation, MiSeq sequencing of 16S rRNA gene amplicons revealed that the phylogenetic composition and structure of microbial communities changed in both samples, and especially Proteobacteria, as the most abundant phylum increased from 45.1 % to 68.2 % in site A, and 50.1 % to 71.3 % in site B, respectively. Some unique OTUs and populations affiliated with Geobacter, Clostridium, Desulfosporosinus and Desulfosporosinus might be involved in Cr (VI) reduction in site A. Furthermore, GeoChip 4.0 (a comprehensive functional gene array) data showed that genes involved in carbon and nitrogen cycling and metal resistance significantly (p < 0.05) increased in site A sediment samples. All the results indicated that indigenous sediment microbial communities might be able to remediate contaminants like Cr (VI), and this information provides possible strategies for future bioremediation of the Lanzhou reach.
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Affiliation(s)
- Zhengsheng Yu
- Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Zhili He
- Department of Microbiology and Plant Biology and Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
| | - Xuanyu Tao
- Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Jizhong Zhou
- Department of Microbiology and Plant Biology and Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Mengxin Zhao
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Xiaowei Zhang
- Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Zhe Zheng
- Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Tong Yuan
- Department of Microbiology and Plant Biology and Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
| | - Pu Liu
- Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Yong Chen
- Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Virgo Nolan
- Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Xiangkai Li
- Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, 730000, China.
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