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Si T, Chen H, Qiu Z, Zhang L, Ohore OE, Zhang S. Bacterial succession in epiphytic biofilms and deciduous layer sediments during Hydrilla verticillata decay: A field investigation. J Environ Sci (China) 2020; 93:193-201. [PMID: 32446455 DOI: 10.1016/j.jes.2020.03.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/29/2020] [Accepted: 03/07/2020] [Indexed: 06/11/2023]
Abstract
Submersed macrophytes decay is an important natural process and has important role in mass and energy flow in aquatic ecosystems. However, little is known about the dynamical changes in nutrients release and bacterial community during submersed macrophyte decay in natural environment. In this study, a field observation was conducted in a wetland dominated with Hydrilla verticillata for 36 days. Increase of H2O2 and malondialdehyde (MDA) content and decrease of soluble proteins concentration were detected in leaves during H. verticillata decay. Meanwhile, ammonium-N, soluble microbial products (SMP) and TOC concentration increased in overlying water. According to bacterial 16S rRNA Illumina sequencing analysis, the Shannon values were lower in epiphytic biofilms than deciduous layer sediments. The relative abundances of Proteobacteria, Cyanobacteria and Actinobacteria were higher in epiphytic biofilms than in deciduous layer sediments (P < 0.05). Co-occurrence network analyses showed that a total of 578 and 845 pairs of correlations (|r| > 0.6) were identified from 122 and 112 genera in epiphytic biofilms and deciduous layer sediments, respectively. According to co-occurrence patterns, eight hubs were mainly from phyla Proteobacteria, Acidobacteria and Parcubacteria in epiphytic biofilms; while 37 hubs from the 14 phyla (Proteobacteria, Bacteroidetes, Acidobacteria, Chloroflexi, et al.) were detected in deciduous layer sediments. Our results indicate that bacterial community in deciduous layer sediments was more susceptible than in epiphytic biofilms during decay process. These data highlight the role of microbial community in deciduous layer sediments on nutrients removal during H. verticillata decay and will provide useful information for wetland management.
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Affiliation(s)
- Tingting Si
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, China
| | - Hezhou Chen
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, China
| | - Zheng Qiu
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, China
| | - Lisha Zhang
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, China
| | - Okugbe Ebiotubo Ohore
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, China
| | - Songhe Zhang
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, China.
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Chroňáková A, Bárta J, Kaštovská E, Urbanová Z, Picek T. Spatial heterogeneity of belowground microbial communities linked to peatland microhabitats with different plant dominants. FEMS Microbiol Ecol 2020; 95:5551480. [PMID: 31425589 DOI: 10.1093/femsec/fiz130] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 08/16/2019] [Indexed: 11/13/2022] Open
Abstract
Peatland vegetation is composed mostly of mosses, graminoids and ericoid shrubs, and these have a distinct impact on peat biogeochemistry. We studied variation in soil microbial communities related to natural peatland microhabitats dominated by Sphagnum, cotton-grass and blueberry. We hypothesized that such microhabitats will be occupied by structurally and functionally different microbial communities, which will vary further during the vegetation season due to changes in temperature and photosynthetic activity of plant dominants. This was addressed using amplicon-based sequencing of prokaryotic and fungal rDNA and qPCR with respect to methane-cycling communities. Fungal communities were highly microhabitat-specific, while prokaryotic communities were additionally directed by soil pH and total N content. Seasonal alternations in microbial community composition were less important; however, they influenced the abundance of methane-cycling communities. Cotton-grass and blueberry bacterial communities contained relatively more α-Proteobacteria but less Chloroflexi, Fibrobacteres, Firmicutes, NC10, OD1 and Spirochaetes than in Sphagnum. Methanogens, syntrophic and anaerobic bacteria (i.e. Clostridiales, Bacteroidales, Opitutae, Chloroflexi and Syntrophorhabdaceae) were suppressed in blueberry indicating greater aeration that enhanced abundance of fungi (mainly Archaeorhizomycetes) and resulted in the highest fungi-to-bacteria ratio. Thus, microhabitats dominated by different vascular plants are inhabited by unique microbial communities, contributing greatly to spatial functional diversity within peatlands.
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Affiliation(s)
- Alica Chroňáková
- Biology Centre, CAS, Institute of Soil Biology and SoWa RI, Na Sádkách 7, České Budějovice 370 05, Czech Republic
| | - Jiří Bárta
- Department of Ecosystem Biology, University of South Bohemia in České Budějovice, Branišovská 1760, České Budějovice 370 05, Czech Republic
| | - Eva Kaštovská
- Department of Ecosystem Biology, University of South Bohemia in České Budějovice, Branišovská 1760, České Budějovice 370 05, Czech Republic
| | - Zuzana Urbanová
- Department of Ecosystem Biology, University of South Bohemia in České Budějovice, Branišovská 1760, České Budějovice 370 05, Czech Republic
| | - Tomáš Picek
- Department of Ecosystem Biology, University of South Bohemia in České Budějovice, Branišovská 1760, České Budějovice 370 05, Czech Republic
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Liu T, Awasthi SK, Duan Y, Zhang Z, Awasthi MK. Effect of fine coal gasification slag on improvement of bacterial diversity community during the pig manure composting. BIORESOURCE TECHNOLOGY 2020; 304:123024. [PMID: 32086035 DOI: 10.1016/j.biortech.2020.123024] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 02/11/2020] [Accepted: 02/12/2020] [Indexed: 06/10/2023]
Abstract
In present study, evaluate the effect of fine coal gasification slag (FCGS) as additive on abundance of bacterial diversity during pig manure composting. The six different dosages of FCGS 0% (T1), 2% (T2), 4% (T3), 6% (T4), 8% (T5) and 10% (T6) (dry weight basis) were mixed with original raw materials for 42 days an aerobic composting. The results indicated that FCGS adopted could affect the succession of bacterial diversity in different ways. Among all treatments, Firmicutes, Proteobacteria, Tenericutes, unidentified_Bacteria, and Actinobacteria were the highest abundance in weighted unifrac distance but Firmicutes; Proteobacteria, Actinobacteria, Bacteroidetes, and Spirochaetes were main bacteria in unweighted unifrac distance. The β-diversity and principal component analysis indicated a significant difference in bacterial diversity in all treatments which T4 obtained difference obviously. Therefore, the results showed that T4 was a potential candidate to enhance significantly abundance of bacterial community in PM compost.
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Affiliation(s)
- Tao Liu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, PR China
| | - Sanjeev Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, PR China
| | - Yumin Duan
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, PR China
| | - Zengqiang Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, PR China
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, PR China.
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Ivanova AA, Beletsky AV, Rakitin AL, Kadnikov VV, Philippov DA, Mardanov AV, Ravin NV, Dedysh SN. Closely Located but Totally Distinct: Highly Contrasting Prokaryotic Diversity Patterns in Raised Bogs and Eutrophic Fens. Microorganisms 2020; 8:microorganisms8040484. [PMID: 32235351 PMCID: PMC7232223 DOI: 10.3390/microorganisms8040484] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 03/25/2020] [Accepted: 03/27/2020] [Indexed: 01/21/2023] Open
Abstract
Large areas in Northern Russia are covered by extensive mires, which represent a complex mosaic of ombrotrophic raised bogs, minerotrophic and eutrophic fens, all in a close proximity to each other. In this paper, we compared microbial diversity patterns in the surface peat layers of the neighbouring raised bogs and eutrophic fens that are located within two geographically remote mire sites in Vologda region using 16S rRNA gene sequencing. Regardless of location, the microbial communities in raised bogs were highly similar to each other but were clearly distinct from those in eutrophic fens. Bogs were dominated by the Acidobacteria (30%–40% of total 16S rRNA gene reads), which belong to the orders Acidobacteriales and Bryobacterales. Other bog-specific bacteria included the Phycisphaera-like group WD2101 and the families Isosphaeraceae and Gemmataceae of the Planctomycetes, orders Opitutales and Pedosphaerales of the Verrucomicrobia and a particular group of alphaproteobacteria within the Rhizobiales. In contrast, fens hosted Anaerolineae-affiliated Chloroflexi, Vicinamibacteria- and Blastocatellia-affiliated Acidobacteria, Rokubacteria, uncultivated group OM190 of the Planctomycetes and several groups of betaproteobacteria. The Patescibacteria were detected in both types of wetlands but their relative abundance was higher in fens. A number of key parameters that define the distribution of particular bacterial groups in mires were identified.
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Affiliation(s)
- Anastasia A. Ivanova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia; (A.A.I.); (S.N.D.)
| | - Alexey V. Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia; (A.V.B.); (A.L.R.); (V.V.K.); (A.V.M.)
| | - Andrey L. Rakitin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia; (A.V.B.); (A.L.R.); (V.V.K.); (A.V.M.)
| | - Vitaly V. Kadnikov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia; (A.V.B.); (A.L.R.); (V.V.K.); (A.V.M.)
| | - Dmitriy A. Philippov
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok 152742, Russia;
| | - Andrey V. Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia; (A.V.B.); (A.L.R.); (V.V.K.); (A.V.M.)
| | - Nikolai V. Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia; (A.V.B.); (A.L.R.); (V.V.K.); (A.V.M.)
- Correspondence:
| | - Svetlana N. Dedysh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia; (A.A.I.); (S.N.D.)
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Potential PGPR Properties of Cellulolytic, Nitrogen-Fixing, Phosphate-Solubilizing Bacteria in Rehabilitated Tropical Forest Soil. Microorganisms 2020; 8:microorganisms8030442. [PMID: 32245141 PMCID: PMC7143980 DOI: 10.3390/microorganisms8030442] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 02/14/2020] [Accepted: 02/20/2020] [Indexed: 11/17/2022] Open
Abstract
In the midst of the major soil degradation and erosion faced by tropical ecosystems, rehabilitated forests are being established to avoid the further deterioration of forest lands. In this context, cellulolytic, nitrogen-fixing (N-fixing), phosphate-solubilizing bacteria are very important functional groups in regulating the elemental cycle and plant nutrition, hence replenishing the nutrient content in forest soils. As is the case for other potential plant growth-promoting (PGP) rhizobacteria, these functional bacteria could have cross-functional abilities or beneficial traits that are essential for plants and can improve their growth. This study was conducted to isolate, identify, and characterize selected PGP properties of these three functional groups of bacteria from tropical rehabilitated forest soils at Universiti Putra Malaysia Bintulu Sarawak Campus, Malaysia. The bacteria were isolated based on their colonial growth on respective functional media, identified using both molecular and selected biochemical properties, and were assessed for their functional quantitative activities as well as PGP properties based on seed germination tests and indole-3-acetic acid (IAA) production. Out of the 15 identified bacterial isolates that exhibited beneficial phenotypic traits, a third belong to the genus Burkholderia and a fifth to Stenotrophomonas sp., with both genera consisting of members from two different functional groups. The results of the experiments confirm the multiple PGP traits of some selected bacterial isolates based on their respective high functional activities, root and shoot lengths, and seedling vigor improvements when bacterized on mung bean seeds, as well as significant IAA production. The results of this study suggest that these functional bacterial strains could potentially be included in bio-fertilizer formulations for crop growth on acid soils.
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Tang A, Haruna AO, Majid NMA, Jalloh MB. Potential PGPR Properties of Cellulolytic, Nitrogen-Fixing, Phosphate-Solubilizing Bacteria in Rehabilitated Tropical Forest Soil. Microorganisms 2020; 8:microorganisms8030442. [PMID: 32245141 DOI: 10.1101/351916] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 02/14/2020] [Accepted: 02/20/2020] [Indexed: 05/22/2023] Open
Abstract
In the midst of the major soil degradation and erosion faced by tropical ecosystems, rehabilitated forests are being established to avoid the further deterioration of forest lands. In this context, cellulolytic, nitrogen-fixing (N-fixing), phosphate-solubilizing bacteria are very important functional groups in regulating the elemental cycle and plant nutrition, hence replenishing the nutrient content in forest soils. As is the case for other potential plant growth-promoting (PGP) rhizobacteria, these functional bacteria could have cross-functional abilities or beneficial traits that are essential for plants and can improve their growth. This study was conducted to isolate, identify, and characterize selected PGP properties of these three functional groups of bacteria from tropical rehabilitated forest soils at Universiti Putra Malaysia Bintulu Sarawak Campus, Malaysia. The bacteria were isolated based on their colonial growth on respective functional media, identified using both molecular and selected biochemical properties, and were assessed for their functional quantitative activities as well as PGP properties based on seed germination tests and indole-3-acetic acid (IAA) production. Out of the 15 identified bacterial isolates that exhibited beneficial phenotypic traits, a third belong to the genus Burkholderia and a fifth to Stenotrophomonas sp., with both genera consisting of members from two different functional groups. The results of the experiments confirm the multiple PGP traits of some selected bacterial isolates based on their respective high functional activities, root and shoot lengths, and seedling vigor improvements when bacterized on mung bean seeds, as well as significant IAA production. The results of this study suggest that these functional bacterial strains could potentially be included in bio-fertilizer formulations for crop growth on acid soils.
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Affiliation(s)
- Amelia Tang
- Faculty of Agriculture and Food Sciences, Universiti Putra Malaysia Bintulu Campus, Bintulu 97008, Sarawak, Malaysia
| | - Ahmed Osumanu Haruna
- Faculty of Agriculture and Food Sciences, Universiti Putra Malaysia Bintulu Campus, Bintulu 97008, Sarawak, Malaysia
- Institute of Tropical Agriculture and Food Security (ITAFoS), Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
- Institute of Tropical Forestry and Forest Products (INTROP), Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Nik Muhamad Ab Majid
- Institute of Tropical Forestry and Forest Products (INTROP), Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Mohamadu Boyie Jalloh
- Faculty of Sustainable Agriculture, Universiti Malaysia Sabah, Sandakan Branch, Locked Bag No. 3, Sandakan 90509, Sabah, Malaysia
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Linking ecology and systematics of acidobacteria: Distinct habitat preferences of the Acidobacteriia and Blastocatellia in tundra soils. PLoS One 2020; 15:e0230157. [PMID: 32182280 PMCID: PMC7077872 DOI: 10.1371/journal.pone.0230157] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 02/22/2020] [Indexed: 12/26/2022] Open
Abstract
The Acidobacteria is one of the major bacterial phyla in soils and peatlands. The currently explored diversity within this phylum is assigned to 15 class-level units, five of which contain described members. The ecologically relevant traits of acidobacteria from different classes remain poorly understood. Here, we compared the patterns of acidobacterial diversity in sandy soils of tundra, along a gradient of increasing vegetation–unfixed aeolian sand, semi-fixed surfaces with mosses and lichens, and mature soil under fully developed plant cover. The Acidobacteria-affiliated 16S rRNA gene sequences retrieved from these soils comprised 11 to 33% of total bacterial reads and belonged mostly to members of the classes Acidobacteriia and Blastocatellia, which displayed opposite habitat preferences. The relative abundance of the Blastocatellia was maximal in unfixed sands and declined in soils of vegetated plots, showing positive correlation with soil pH and negative correlation with carbon and nitrogen availability. An opposite tendency was characteristic for the Acidobacteriia. Most Blastocatellia-affiliated reads belonged to as-yet-undescribed members of the family Arenimicrobiaceae, which appears to be characteristic for dry, depleted in organic matter soil habitats. The pool of Acidobacteriia-affiliated sequences, apart from Acidobacteriaceae- and Bryobacteraceae-related reads, had a large proportion of sequences from as-yet-undescribed families, which seem to specialize in degrading plant-derived organic matter. This analysis reveals sandy soils of tundra as a source of novel acidobacterial diversity and provides an insight into the ecological preferences of different taxonomic groups within this phylum.
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Li Y, Liu Y, Yong X, Wu X, Jia H, Wong JWC, Wu H, Zhou J. Odor emission and microbial community succession during biogas residue composting covered with a molecular membrane. BIORESOURCE TECHNOLOGY 2020; 297:122518. [PMID: 31812915 DOI: 10.1016/j.biortech.2019.122518] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/26/2019] [Accepted: 11/27/2019] [Indexed: 06/10/2023]
Abstract
A membrane-covered composting system was used to investigate the odor emission and microbial community succession during biogas residue composting. Results showed that in comparison with the control (CK) group, the NH3 and H2S emissions outside the membrane of the membrane-covered (CT) group decreased by 58.64% and 38.13%, respectively. The nitrogen preservation rate of the CT group was increased by 17.27% in comparison with the CK group. Moreover, the ammonium nitrogen and nitrate nitrogen contents of the CT group were 37.68% and 11.77% higher than those of the CK group, respectively. Microbial analysis showed that the average abundance and co-occurrence rate of ammonification bacteria dominated by Pseudomonas and Bacillus in the CT group were lower than those in the CK group, and the abundance of anaerobic sulfate-reducing bacteria (SRB) dominated by Desulfovibrio in the CT group was higher than that in the CK group.
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Affiliation(s)
- Yinchao Li
- Bioenergy Research Institute, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, Jiangsu 211816, China
| | - Yongdi Liu
- Bioenergy Research Institute, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, Jiangsu 211816, China
| | - Xiaoyu Yong
- Bioenergy Research Institute, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, Jiangsu 211816, China
| | - Xiayuan Wu
- Bioenergy Research Institute, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, Jiangsu 211816, China
| | - Honghua Jia
- Bioenergy Research Institute, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, Jiangsu 211816, China
| | - Jonathan W C Wong
- Institute of Bioresource and Agriculture, Hong Kong Baptist University, Hong Kong Special Administrative Region
| | - Hao Wu
- Bioenergy Research Institute, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, Jiangsu 211816, China
| | - Jun Zhou
- Bioenergy Research Institute, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, Jiangsu 211816, China.
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Li J, Xing W, Bao H, Wang J, Tong X, Zhang H, Luo W, Wu F. Impact of pine leaf biochar amendment on bacterial dynamics and correlation of environmental factors during pig manure composting. BIORESOURCE TECHNOLOGY 2019; 293:122031. [PMID: 31476566 DOI: 10.1016/j.biortech.2019.122031] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 08/14/2019] [Accepted: 08/16/2019] [Indexed: 06/10/2023]
Abstract
The influence of pine leaf biochar (PLB) amendment on bacterial community succession and its correlation with physic-chemical parameters during pig manure (PM) composting was evaluated. The five different dosages of PLB [at 0% (T1), 2.5% (T2), 5% (T3), 10% (T4) and 15% (T5)] mixed with initial composting mass were conducted to composting for 50 days. The present study indicated that bacterial diversity was significantly (p < 0.05) higher in PLB amended treatments than the control, but T4 treatment showed the highest among the all PLB applied treatment. Firmicutes, Actinobacteria, Proteobacteria and Bacteroidete were four most abundant phyla of all the treatments. Furthermore, redundancy analysis showed that the bacterial community were significantly (p < 0.05) positively correlated with temperature, pH, TOC, CO2 and NH3 emissions, while they were negatively correlated with the N2O and CH4 emission. Overall, the results suggested that the addition of 10% PLB (T4 treatment) was a potential option to enhance the composting efficiency with significantly greater abundance of bacterial community and finally improved the compost quality.
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Affiliation(s)
- Jiao Li
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling 712100, Shaanxi, China
| | - Wenjing Xing
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling 712100, Shaanxi, China
| | - Huanyu Bao
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling 712100, Shaanxi, China
| | - Jinfeng Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling 712100, Shaanxi, China
| | - Xiaogang Tong
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - He Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling 712100, Shaanxi, China
| | - Wanqing Luo
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling 712100, Shaanxi, China
| | - Fuyong Wu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling 712100, Shaanxi, China.
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Sivadon P, Barnier C, Urios L, Grimaud R. Biofilm formation as a microbial strategy to assimilate particulate substrates. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:749-764. [PMID: 31342619 DOI: 10.1111/1758-2229.12785] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 07/15/2019] [Accepted: 07/21/2019] [Indexed: 06/10/2023]
Abstract
In most ecosystems, a large part of the organic carbon is not solubilized in the water phase. Rather, it occurs as particles made of aggregated hydrophobic and/or polymeric natural or man-made organic compounds. These particulate substrates are degraded by extracellular digestion/solubilization implemented by heterotrophic bacteria that form biofilms on them. Organic particle-degrading biofilms are widespread and have been observed in aquatic and terrestrial natural ecosystems, in polluted and man-driven environments and in the digestive tracts of animals. They have central ecological functions as they are major players in carbon recycling and pollution removal. The aim of this review is to highlight bacterial adhesion and biofilm formation as central mechanisms to exploit the nutritive potential of organic particles. It focuses on the mechanisms that allow access and assimilation of non-dissolved organic carbon, and considers the advantage provided by biofilms for gaining a net benefit from feeding on particulate substrates. Cooperative and competitive interactions taking place in biofilms feeding on particulate substrates are also discussed.
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Affiliation(s)
- Pierre Sivadon
- CNRS/Université de Pau et des Pays de l'Adour/E2S UPPA, Institut des Sciences Analytiques et de Physico-Chimie pour l'Environnement et les Matériaux UMR5254, Pau, 64000, France
| | - Claudie Barnier
- CNRS/Université de Pau et des Pays de l'Adour/E2S UPPA, Institut des Sciences Analytiques et de Physico-Chimie pour l'Environnement et les Matériaux UMR5254, Pau, 64000, France
| | - Laurent Urios
- CNRS/Université de Pau et des Pays de l'Adour/E2S UPPA, Institut des Sciences Analytiques et de Physico-Chimie pour l'Environnement et les Matériaux UMR5254, Pau, 64000, France
| | - Régis Grimaud
- CNRS/Université de Pau et des Pays de l'Adour/E2S UPPA, Institut des Sciences Analytiques et de Physico-Chimie pour l'Environnement et les Matériaux UMR5254, Pau, 64000, France
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Zhang C, Zhou T, Zhu L, Juhasz A, Du Z, Li B, Wang J, Wang J, Sun Y. Response of soil microbes after direct contact with pyraclostrobin in fluvo-aquic soil. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 255:113164. [PMID: 31522004 DOI: 10.1016/j.envpol.2019.113164] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 09/02/2019] [Accepted: 09/02/2019] [Indexed: 06/10/2023]
Abstract
Agricultural chemicals affect the daily life of food production. However, the abuse of pesticides led to the damage to the environment. Pyraclostrobin (PYR) is commonly used strobilurin fungicide which inhibits fungal respiration through mitochondrial cytochrome-b and c1 inhibition. There is increasing concerns that PYR may adversely impact the environment. Although impacts on ecological receptors have been detailed, little information is available regarding the toxicological impact of PYR on soil microbial community dynamics and functioning. Understanding the potential impact on soil microbial populations is important. The activity of enzymes (urease, dehydrogenase, and β-glucosidase) and diversity of microbial community structure using high-throughput 16S rRNA sequencing were evaluated at different soil-PYR concentrations (0.1, 1.0, and 2.5 mg/kg) over a 48 day exposure period. Urease activity remained stable in general. Pyraclostrobin inhibited dehydrogenase activity during the exposure period. The β-glucosidase activity was inhibited on day 28 and induced on day 48 at 1.0 and 2.5 mg/kg. The genera Gp6, Exiguobacterium, Gp4, and Gemmatimonas were both the dominant genera and significantly changed genera. Pyraclostrobin had different level of influence on soil microbes containg their enzyme activity and community structure. The purpose of the current study was to examine the impact of PYR addition on soil enzymes as an indicator of soil health and to have complementary data on the impact of microbial populations. Furthermore, the study may also be the guide for further rational pesticide selection.
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Affiliation(s)
- Cheng Zhang
- College of Resources and Environment, Shandong Agricultural University, Key Laboratory of Agricultural Environment in Universities of Shandong, National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Daizong Road 61, Taian, 271018, PR China.
| | - Tongtong Zhou
- College of Resources and Environment, Shandong Agricultural University, Key Laboratory of Agricultural Environment in Universities of Shandong, National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Daizong Road 61, Taian, 271018, PR China.
| | - Lusheng Zhu
- College of Resources and Environment, Shandong Agricultural University, Key Laboratory of Agricultural Environment in Universities of Shandong, National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Daizong Road 61, Taian, 271018, PR China.
| | - Albert Juhasz
- Future Industries Institute, Centre for Environmental Risk Assessment and Remediation, University of South Australia, Mawson Lakes, SA 5095, Australia.
| | - Zhongkun Du
- College of Resources and Environment, Shandong Agricultural University, Key Laboratory of Agricultural Environment in Universities of Shandong, National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Daizong Road 61, Taian, 271018, PR China.
| | - Bing Li
- College of Resources and Environment, Shandong Agricultural University, Key Laboratory of Agricultural Environment in Universities of Shandong, National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Daizong Road 61, Taian, 271018, PR China.
| | - Jun Wang
- College of Resources and Environment, Shandong Agricultural University, Key Laboratory of Agricultural Environment in Universities of Shandong, National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Daizong Road 61, Taian, 271018, PR China.
| | - Jinhua Wang
- College of Resources and Environment, Shandong Agricultural University, Key Laboratory of Agricultural Environment in Universities of Shandong, National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Daizong Road 61, Taian, 271018, PR China.
| | - Yan'an Sun
- College of Resources and Environment, Shandong Agricultural University, Key Laboratory of Agricultural Environment in Universities of Shandong, National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Daizong Road 61, Taian, 271018, PR China.
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Li P, Zhang Y, Meng Q, Liu Y, Tuyiringire D, Chen Z, Liang S. Effects of trichloroethylene stress on the microbiological characteristics of Mollisol. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 184:109595. [PMID: 31470249 DOI: 10.1016/j.ecoenv.2019.109595] [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: 04/20/2019] [Revised: 08/17/2019] [Accepted: 08/20/2019] [Indexed: 06/10/2023]
Abstract
Trichloroethylene (TCE), one of 129 kinds of priority pollutants, is the most common halogenated organic pollutant in the environment. To explore the changes in soil physicochemical properties and biological activities then clarify the effects of these factors on bacterial, fungal and actinomycetes communities in Mollisol under TCE stress is the significance of our research. The results indicated that when TCE concentration was greater than 10 mg kg-1, soil quality declined and soil decomposition of organic matter and cycling of mineral nutrients were inhibited through an effect on soil microbial biomass. Operational taxonomic units (OTUs) richness of the bacteria in Mollisol was altered by TCE contamination. The SChao1 and HShannon indices of bacterial communities in Mollisol decreased when 40 mg kg-1 TCE was applied. Meanwhile, the OTU richness of fungi in Mollisol was altered by TCE contamination. The HShannon indices of the fungal communities in Mollisol were inhibited by higher TCE concentrations (20 and 40 mg kg-1 TCE). TCE altered the content of some bacteria, fungi and actinomycetes involved in soil carbon and nitrogen cycling and metabolism, such as Acidobacteria, Proteobacteria, Planctomycetes, Chytridiomycota, Streptomycetales, Pseudonocardiales, Propionibacteriales and Rhizobiales, and thus influenced nutrient cycling and the process of energy metabolism in Mollisol. In addition, redundancy analysis (RDA) results indicated that physicochemical properties and biological activities under TCE contamination significantly affected soil microbial community composition thus confirming that TCE interfered with the carbon and nitrogen cycling and metabolism of soil microorganisms. The results of this study are of great importance for revealing the effects of TCE stress on the microbiological characteristics of Mollisol, and also provide more useful information for determining the potential ecological risk of organic pollutants in Mollisol.
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Affiliation(s)
- Pengfei Li
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China.
| | - Ying Zhang
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China.
| | - Qingjuan Meng
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Ying Liu
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Diogene Tuyiringire
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Zhaobo Chen
- College of Environment and Resources, Dalian Minzu University, 18 Liaohe West Road, Dalian, 116600, China
| | - Shichao Liang
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
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63
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Gadkari PS, McGuinness LR, Männistö MK, Kerkhof LJ, Häggblom MM. Arctic tundra soil bacterial communities active at subzero temperatures detected by stable isotope probing. FEMS Microbiol Ecol 2019; 96:5645228. [DOI: 10.1093/femsec/fiz192] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 11/26/2019] [Indexed: 12/14/2022] Open
Abstract
ABSTRACT
Arctic soils store vast amounts of carbon and are subject to intense climate change. While the effects of thaw on the composition and activities of Arctic tundra microorganisms has been examined extensively, little is known about the consequences of temperature fluctuations within the subzero range in seasonally frozen or permafrost soils. This study identified tundra soil bacteria active at subzero temperatures using stable isotope probing (SIP). Soils from Kilpisjärvi, Finland, were amended with 13C-cellobiose and incubated at 0, −4 and −16°C for up to 40 weeks. 16S rRNA gene sequence analysis of 13C-labelled DNA revealed distinct subzero-active bacterial taxa. The SIP experiments demonstrated that diverse bacteria, including members of Candidatus Saccharibacteria, Melioribacteraceae, Verrucomicrobiaceae, Burkholderiaceae, Acetobacteraceae, Armatimonadaceae and Planctomycetaceae, were capable of synthesising 13C-DNA at subzero temperatures. Differences in subzero temperature optima were observed, for example, with members of Oxalobacteraceae and Rhizobiaceae found to be more active at 0°C than at −4°C or −16°C, whereas Melioribacteriaceae were active at all subzero temperatures tested. Phylogeny of 13C-labelled 16S rRNA genes from the Melioribacteriaceae, Verrucomicrobiaceae and Candidatus Saccharibacteria suggested that these taxa formed subzero-active clusters closely related to members from other cryo-environments. This study demonstrates that subzero temperatures impact active bacterial community composition and activity, which may influence biogeochemical cycles.
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Affiliation(s)
- Preshita S Gadkari
- School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick NJ 08901, USA
| | - Lora R McGuinness
- Department of Marine and Coastal Sciences, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Minna K Männistö
- Natural Resources Institute Finland, P.O. Box 16, FI-96301 Rovaniemi, Finland
| | - Lee J Kerkhof
- Department of Marine and Coastal Sciences, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Max M Häggblom
- School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick NJ 08901, USA
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64
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Tian W, Wang H, Xiang X, Wang R, Xu Y. Structural Variations of Bacterial Community Driven by Sphagnum Microhabitat Differentiation in a Subalpine Peatland. Front Microbiol 2019; 10:1661. [PMID: 31396183 PMCID: PMC6667737 DOI: 10.3389/fmicb.2019.01661] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 07/04/2019] [Indexed: 11/13/2022] Open
Abstract
Sphagnum microbiomes play an important role in the northern peatland ecosystems. However, information about above and belowground microbiomes related to Sphagnum at subtropical area remains largely limited. In this study, microbial communities from Sphagnum palustre peat, S. palustre green part, and S. palustre brown part at the Dajiuhu Peatland, in central China were investigated via 16S rRNA gene amplicon sequencing. Results indicated that Alphaproteobacteria was the dominant class in all samples, and the classes Acidobacteria and Gammaproteobacteria were abundant in S. palustre peat and S. palustre brown part samples, respectively. In contrast, the class Cyanobacteria dominated in S. palustre green part samples. Microhabitat differentiation mainly contributes to structural differences of bacterial microbiome. In the S. palustre peat, microbial communities were significantly shaped by water table and total nitrogen content. Our study is a systematical investigation on above and belowground bacterial microbiome in a subalpine Sphagnum peatland and the results offer new knowledge about the distribution of bacterial microbiome associated with different microhabitats in subtropical area.
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Affiliation(s)
- Wen Tian
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Hongmei Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
- Laboratory of Basin Hydrology and Wetland Eco-Restoration, China University of Geosciences, Wuhan, China
| | - Xing Xiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Ruicheng Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Ying Xu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
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65
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Shi L, Du R, Peng Y. Achieving partial denitrification using carbon sources in domestic wastewater with waste-activated sludge as inoculum. BIORESOURCE TECHNOLOGY 2019; 283:18-27. [PMID: 30897389 DOI: 10.1016/j.biortech.2019.03.063] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 03/10/2019] [Accepted: 03/12/2019] [Indexed: 06/09/2023]
Abstract
Partial denitrification (PD, nitrate → nitrite) using carbon sources in domestic wastewater with waste-activated sludge as inoculum was firstly achieved in this study. Through controlling influent pH at about 9.0 and anoxic reaction time of 1 h in the start-up, the nitrite (NO2--N) production reached as high as 25.2 mg/L, with influent nitrate (NO3--N) of about 30 mg/L and chemical oxygen demand (COD) to NO3--N ratio of 5.9. Furthermore, PD performance remained stable without pH control during subsequent operations. Efficient NO2--N production was closely related to the consumed amount of readily biodegradable COD (Ss) fraction, with optimal Ss/NO3--N ratio of about 3.5. Thauera (19.1%), norank_f__Xanthomonadaceae (5.2%), and Thiobacillus (5.0%) were enriched during the 208-day operation, which may be responsible for high NO2--N production. These findings provided a novel strategy for promoting mainstream PD/Anammox application, without additional nitrite-accumulating denitrifying sludge and external carbon sources.
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Affiliation(s)
- Liangliang Shi
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Engineering Research Center of Beijing, Beijing University of Technology, Beijing 100124, China
| | - Rui Du
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Engineering Research Center of Beijing, Beijing University of Technology, Beijing 100124, China
| | - Yongzhen Peng
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Engineering Research Center of Beijing, Beijing University of Technology, Beijing 100124, China.
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66
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Duan Y, Awasthi SK, Liu T, Verma S, Wang Q, Chen H, Ren X, Zhang Z, Awasthi MK. Positive impact of biochar alone and combined with bacterial consortium amendment on improvement of bacterial community during cow manure composting. BIORESOURCE TECHNOLOGY 2019; 280:79-87. [PMID: 30759405 DOI: 10.1016/j.biortech.2019.02.026] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 02/03/2019] [Accepted: 02/04/2019] [Indexed: 06/09/2023]
Abstract
The present work studied to evaluate the effectiveness under the interaction of bacterial consortium and biochar applied to give impetus to bacterial community activities among cow manure composting. High-throughput sequencing technique and six treatments were carried out: T2, T3 and T6 were single apply of bacteria culture (C), 12%wood biochar (12%WB) and 12%wheat straw biochar (12%WSB), respectively, while T4 and T5 were bacterial consortium combined with 12%WB and 12%WSB respectively, and T1 was used as control. The conclusion shows that the richness of bacterial community were most prosperity in T5 and T4 that in line with the statistical analysis angle of curves and cluster. The dominate phyla of Firmicutes, Proteobacteria and Bacteroidetes were accounted to 31.36%, 34.79% and 33.85%, the superior genera were Dysgonomonas (16.55%), Empedobater (9.39%), Atopostipes (13.42%), Tissierella (8.25%), Marinimicrobium (14.45%) and Pseudomonas (9%). Overall, bacterial consortium combined with biochar could stimulate microbe activity to accelerate degradation, enhance richness and alter specific selection of bacterial community.
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Affiliation(s)
- Yumin Duan
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Sanjeev Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Tao Liu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Shivpal Verma
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Quan Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Hongyu Chen
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Xiuna Ren
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Zengqiang Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, China.
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67
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Tao K, Zhang X, Chen X, Liu X, Hu X, Yuan X. Response of soil bacterial community to bioaugmentation with a plant residue-immobilized bacterial consortium for crude oil removal. CHEMOSPHERE 2019; 222:831-838. [PMID: 30743234 DOI: 10.1016/j.chemosphere.2019.01.133] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 12/31/2018] [Accepted: 01/23/2019] [Indexed: 05/23/2023]
Abstract
Both the crude oil removal efficiency of the Eichhornia crassipes dried straw-immobilized bacterial consortium and shifts in soil bacterial community in response to the bioaugmentation strategy were unmasked in this study. After 30 days of bioremediation, total petroleum hydrocarbon in soil was determined and immobilized consortium showed a removal percentage (51.7%) better than either Eichhornia crassipes dried powder (37.0%) or bacteria solution (36.0%) alone. Bacterial community and soil properties analyses demonstrated that the relative abundances of Cytophagales and Rhizobiales increased with increasing total organic carbon and total nitrogen contents because of the addition of Eichhornia crassipes dried powder. The genus Burkholderia which may play a key role in hydrocarbon degradation among the inoculated bacterial consortium proliferated when immobilized on the Eichhornia crassipes dried powder. Such a cell immobilization technology using plant residue materials as carriers helps to improve soil fertility and mitigate competition between indigenous and inoculated microorganisms for nutrients, which offers a promising way to enhance the removal of crude oil from contaminated soils.
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Affiliation(s)
- Kaiyun Tao
- Shanghai Institute of Geological Survey, No.930, LingShi Road, JingAn District, Shanghai 200072, China
| | - Xinying Zhang
- Laboratory of Environmental Remediation, College of Environmental and Chemical Engineering, Shanghai University, No.99, ShangDa Road, BaoShan District, Shanghai 200444, China
| | - Xueping Chen
- Laboratory of Environmental Remediation, College of Environmental and Chemical Engineering, Shanghai University, No.99, ShangDa Road, BaoShan District, Shanghai 200444, China.
| | - Xiaoyan Liu
- Laboratory of Environmental Remediation, College of Environmental and Chemical Engineering, Shanghai University, No.99, ShangDa Road, BaoShan District, Shanghai 200444, China.
| | - Xiaoxin Hu
- SGIDI Engineering Consulting (Group) Co., Ltd, No.38, ShuiFeng Road, YangPu District, Shanghai 200093, China
| | - Xiaoyu Yuan
- Laboratory of Environmental Remediation, College of Environmental and Chemical Engineering, Shanghai University, No.99, ShangDa Road, BaoShan District, Shanghai 200444, China
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Oshkin IY, Kulichevskaya IS, Rijpstra WIC, Sinninghe Damsté JS, Rakitin AL, Ravin NV, Dedysh SN. Granulicella sibirica sp. nov., a psychrotolerant acidobacterium isolated from an organic soil layer in forested tundra, West Siberia. Int J Syst Evol Microbiol 2019; 69:1195-1201. [PMID: 30775959 DOI: 10.1099/ijsem.0.003290] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
An isolate of strictly aerobic, pale-pink pigmented bacteria, strain AF10T, was obtained from an organic soil layer in forested tundra, Nadym region, West Siberia. Cells of strain AF10T were Gram-negative, non-motile rods that produced an amorphous extracellular polysaccharide-like substance and formed large cell aggregates in old cultures. These bacteria were chemoorganotrophic, mildly acidophilic and psychrotolerant, and grew between pH 3.5 and 7.0 (optimum, pH 4.5-5.0) and at temperatures between 2 and 30 °C. The preferred growth substrates were sugars and some polysaccharides. The major fatty acids were iso-C15 : 0, C16 : 0, C16 : 1∆9 c and 13,16-dimethyl octacosanedioic acid. The genome of strain AF10T was 6.14 Mbp in size and encoded a wide repertoire of carbohydrate active enzymes. The genomic DNA G+C content was 59.8 mol%. Phylogenetic analysis indicated that strain AF10T is a member of the genus Granulicella, family Acidobacteriaceae, but displays 94.4-98.0 % 16S rRNA gene sequence similarity to currently described members of this genus. On the basis of phenotypic, chemotaxonomic, phylogenetic and genomic analyses, we propose to classify this bacterium as representing a novel species of the genus Granulicella, Granulicellasibirica sp. nov. Strain AF10T (=DSM 104461T=VKM B-3276T) is the type strain.
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Affiliation(s)
- Igor Y Oshkin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Irina S Kulichevskaya
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - W Irene C Rijpstra
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Utrecht University, 1790 AB Den Burg, The Netherlands
| | - Jaap S Sinninghe Damsté
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Utrecht University, 1790 AB Den Burg, The Netherlands.,Faculty of Geosciences, Department of Earth Sciences, Geochemistry, Utrecht University, Utrecht, The Netherlands
| | - Andrey L Rakitin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Nikolai V Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Svetlana N Dedysh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
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69
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Kügler S, Cooper RE, Wegner CE, Mohr JF, Wichard T, Küsel K. Iron-organic matter complexes accelerate microbial iron cycling in an iron-rich fen. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 646:972-988. [PMID: 30235650 DOI: 10.1016/j.scitotenv.2018.07.258] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 07/09/2018] [Accepted: 07/18/2018] [Indexed: 06/08/2023]
Abstract
The accessibility of iron (Fe) species for microbial processes is dependent on solubility and redox state, which are influenced by complexation with dissolved organic matter (DOM) and water-extractable organic matter (WEOM). We evaluated the complexation of these pools of organic matter to soluble Fe(II) and Fe(III) in the slightly acidic Schlöppnerbrunnen fen and subsequent effects on Fe(II) oxidation and Fe(III) reduction. We found the majority of soluble Fe(II) and Fe(III) is complexed to DOM. High-resolution mass spectrometry identified potential complexing partners in peat-derived water extracts (PWE), including compound classes known to function as ligands or electron shuttles, like tannins and sulfur-containing compounds. Furthermore, we observed clear differences in the stability of Fe(II)- and Fe(III)-DOM, with more labile complexes dominating the upper, oxic layers (0-10 cm) and more stable complexes in lower, anoxic layers (15-30 cm). Metal isotope-coded profiling identified a single potential chemical formula (C42H57O13N9Fe2) associated with a stable Fe-DOM complex. Fe(III) reduction and Fe(II) oxidation incubations with Geobacter sulfurreducens PCA and Shewanella oneidensis MR-1 or Sideroxydans CL-21, respectively, were used to determine the influence of Fe-DOM complexes on Fe cycling rates. The addition of PWE led to a 2.3-fold increase in Fe(III) reduction rates and 0.5-fold increase in Fe(II) oxidation rates, indicating Fe-DOM complexes greatly influence microbial Fe cycling by potentially serving as electron shuttles. Molecular analyses revealed Fe(III)-reducing and Fe(II)-oxidizing bacteria co-exist across all depths, in approximately equal proportions (representing 0.1-1.0% of the total microbial community), despite observed changes in redox potential. The activity of Fe(III)-reducing bacteria might explain the presence of the detected Fe(II) stabilized via complexation with DOM even under oxic conditions in upper peat layers. Therefore, these Fe(II)-DOM complexes can be recycled by microaerophilic Fe(II)-oxidizers. Taken together, these results suggest Fe-DOM complexation in the fen accelerates microbial-mediated redox processes across the entire redox continuum.
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Affiliation(s)
- Stefan Kügler
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Jena 07743, Germany; Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Jena 07743, Germany
| | - Rebecca E Cooper
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Jena 07743, Germany
| | - Carl-Eric Wegner
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Jena 07743, Germany
| | - Jan Frieder Mohr
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Jena 07743, Germany
| | - Thomas Wichard
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Jena 07743, Germany
| | - Kirsten Küsel
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Jena 07743, Germany; The German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig 04103, Germany.
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70
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Too CC, Keller A, Sickel W, Lee SM, Yule CM. Microbial Community Structure in a Malaysian Tropical Peat Swamp Forest: The Influence of Tree Species and Depth. Front Microbiol 2018; 9:2859. [PMID: 30564202 PMCID: PMC6288306 DOI: 10.3389/fmicb.2018.02859] [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: 06/28/2018] [Accepted: 11/06/2018] [Indexed: 02/01/2023] Open
Abstract
Tropical peat swamp forests sequester globally significant stores of carbon in deep layers of waterlogged, anoxic, acidic and nutrient-depleted peat. The roles of microbes in supporting these forests through the formation of peat, carbon sequestration and nutrient cycling are virtually unknown. This study investigated physicochemical peat properties and microbial diversity between three dominant tree species: Shorea uliginosa (Dipterocarpaceae), Koompassia malaccensis (legumes associated with nitrogen-fixing bacteria), Eleiodoxa conferta (palm) and depths (surface, 45 and 90 cm) using microbial 16S rRNA gene amplicon sequencing. Water pH, oxygen, nitrogen, phosphorus, total phenolic contents and C/N ratio differed significantly between depths, but not tree species. Depth also strongly influenced microbial diversity and composition, while both depth and tree species exhibited significant impact on the archaeal communities. Microbial diversity was highest at the surface, where fresh leaf litter accumulates, and nutrient supply is guaranteed. Nitrogen was the core parameter correlating to microbial communities, but the interactive effects from various environmental variables displayed significant correlation to relative abundance of major microbial groups. Proteobacteria was the dominant phylum and the most abundant genus, Rhodoplanes, might be involved in nitrogen fixation. The most abundant methanogens and methanotrophs affiliated, respectively, to families Methanomassiliicoccaceae and Methylocystaceae. Our results demonstrated diverse microbial communities and provide valuable insights on microbial ecology in these extreme ecosystems.
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Affiliation(s)
- Chin Chin Too
- School of Science, Monash University Malaysia, Subang Jaya, Malaysia
| | - Alexander Keller
- Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Würzburg, Germany.,Center for Computational and Theoretical Biology, University of Würzburg, Würzburg, Germany
| | - Wiebke Sickel
- Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Sui Mae Lee
- School of Science, Monash University Malaysia, Subang Jaya, Malaysia.,Tropical Medicine & Biology Multidisciplinary Platform, Monash University Malaysia, Subang Jaya, Malaysia
| | - Catherine M Yule
- School of Science, Monash University Malaysia, Subang Jaya, Malaysia.,School of Science and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, Australia
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71
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Belova SE, Ravin NV, Pankratov TA, Rakitin AL, Ivanova AA, Beletsky AV, Mardanov AV, Sinninghe Damsté JS, Dedysh SN. Hydrolytic Capabilities as a Key to Environmental Success: Chitinolytic and Cellulolytic Acidobacteria From Acidic Sub-arctic Soils and Boreal Peatlands. Front Microbiol 2018; 9:2775. [PMID: 30510549 PMCID: PMC6252331 DOI: 10.3389/fmicb.2018.02775] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Accepted: 10/29/2018] [Indexed: 11/13/2022] Open
Abstract
Members of the Acidobacteria are among the most efficient colonizers of acidic terrestrial habitats but the key traits underlying their environmental fitness remain to be understood. We analyzed indigenous assemblages of Acidobacteria in a lichen-covered acidic (pH 4.1) soil of forested tundra dominated by uncultivated members of subdivision 1. An isolate of these bacteria with cells occurring within saccular chambers, strain SBC82T, was obtained. The genome of strain SBC82T consists of a 7.11-Mb chromosome and four megaplasmids, and encodes a wide repertoire of enzymes involved in degradation of chitin, cellulose, and xylan. Among those, four secreted chitinases affiliated with the glycoside hydrolase family GH18 were identified. Strain SBC82T utilized amorphous chitin as a source of carbon and nitrogen; the respective enzyme activities were detected in tests with synthetic substrates. Chitinolytic capability was also confirmed for another phylogenetically related acidobacterium isolated from a Sphagnum peat bog, strain CCO287. As revealed by metatranscriptomic analysis of chitin-amended peat, 16S rRNA reads from these acidobacteria increased in response to chitin availability. Strains SBC82T and CCO287 were assigned to a novel genus and species, Acidisarcina polymorpha gen. nov., sp. nov. Members of this genus colonize acidic soils and peatlands and specialize in degrading complex polysaccharides.
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Affiliation(s)
- Svetlana E Belova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Nikolai V Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | | | - Andrey L Rakitin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Anastasia A Ivanova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Alexey V Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Andrey V Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Jaap S Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University, Den Burg, Netherlands.,Geochemistry, Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, Netherlands
| | - Svetlana N Dedysh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
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72
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Vavilin VA, Rytov SV, Lokshina LY. Modelling the specific pathway of CH 4 and CO 2 formation using carbon isotope fractionation: an example for a boreal mesotrophic fen. ISOTOPES IN ENVIRONMENTAL AND HEALTH STUDIES 2018; 54:475-493. [PMID: 29807459 DOI: 10.1080/10256016.2018.1478820] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 03/17/2018] [Indexed: 06/08/2023]
Abstract
We described mathematically the process of peat methanization in a boreal mesotrophic fen. Gaseous and dissolved CH4 and CO2 as well as their δ13C signatures were considered in the dynamic equations for incubation bottles. In accordance with the model, acetate, H2, and CO2 were produced during cellulose hydrolysis and acidogenesis. 13C/12C in CO2 was a key variable reflecting dynamic changes in the rates of cellulose hydrolysis and acidogenesis, acetoclastic and hydrogenotrophic methanogenesis. As CO2 is the substrate in hydrogenotrophic methanogenesis, δ13C-CO2 increased from the start till the dissolved hydrogen concentration became very low. Thereafter, the rate of acetoclastic methanogenesis with the significant current acetate concentration dominated over the rate of hydrogenotrophic methanogenesis leading to the decreasing δ13C-CO2 and the increasing δ13C-CH4. The model was validated by describing the system's dynamics under strong and weak inhibition of acetoclastic and hydrogenotrophic methanogenesis by methyl fluoride, respectively. During peat methanization at the lowered temperature of 10 °C, the processes of hydrogenotrophic methanogenesis and homoacetogenesis competing for H2 may occur. However, based on dynamics of the carbon isotope signatures, especially on dynamics of δ13C-CO2, the model showed no significant contribution of homoacetogens in peat methanization.
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Affiliation(s)
- Vasily A Vavilin
- a Ecological Department , Water Problems Institute, Russian Academy of Sciences , Moscow , Russian Federation
| | - Sergey V Rytov
- a Ecological Department , Water Problems Institute, Russian Academy of Sciences , Moscow , Russian Federation
| | - Lyudmila Y Lokshina
- a Ecological Department , Water Problems Institute, Russian Academy of Sciences , Moscow , Russian Federation
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73
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Genome-centric view of carbon processing in thawing permafrost. Nature 2018; 560:49-54. [PMID: 30013118 DOI: 10.1038/s41586-018-0338-1] [Citation(s) in RCA: 212] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 06/05/2018] [Indexed: 11/09/2022]
Abstract
As global temperatures rise, large amounts of carbon sequestered in permafrost are becoming available for microbial degradation. Accurate prediction of carbon gas emissions from thawing permafrost is limited by our understanding of these microbial communities. Here we use metagenomic sequencing of 214 samples from a permafrost thaw gradient to recover 1,529 metagenome-assembled genomes, including many from phyla with poor genomic representation. These genomes reflect the diversity of this complex ecosystem, with genus-level representatives for more than sixty per cent of the community. Meta-omic analysis revealed key populations involved in the degradation of organic matter, including bacteria whose genomes encode a previously undescribed fungal pathway for xylose degradation. Microbial and geochemical data highlight lineages that correlate with the production of greenhouse gases and indicate novel syntrophic relationships. Our findings link changing biogeochemistry to specific microbial lineages involved in carbon processing, and provide key information for predicting the effects of climate change on permafrost systems.
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74
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Ma S, Fang C, Sun X, Han L, He X, Huang G. Bacterial community succession during pig manure and wheat straw aerobic composting covered with a semi-permeable membrane under slight positive pressure. BIORESOURCE TECHNOLOGY 2018; 259:221-227. [PMID: 29558720 DOI: 10.1016/j.biortech.2018.03.054] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 03/08/2018] [Accepted: 03/11/2018] [Indexed: 06/08/2023]
Abstract
Bacteria play an important role in organic matter degradation and maturity during aerobic composting. This study analyzed composting with or without a membrane cover in laboratory-scale aerobic composting reactor systems. 16S rRNA gene analysis was used to study the bacterial community succession during composting. The richness of the bacterial community decreased and the diversity increased after covering with a semi-permeable membrane and applying a slight positive pressure. Principal components analysis based on operational taxonomic units could distinguish the main composting phases. Linear Discriminant Analysis Effect Size analysis indicated that covering with a semi-permeable membrane reduced the relative abundance of anaerobic Clostridiales and pathogenic Pseudomonas and increased the abundance of Cellvibrionales. In membrane-covered aerobic composting systems, the relative abundance of some bacteria could be affected, especially anaerobic bacteria. Covering could effectively promote fermentation, reduce emissions and ensure organic fertilizer quality.
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Affiliation(s)
- Shuangshuang Ma
- Laboratory of Biomass and Bioprocessing Engineering, College of Engineering, China Agricultural University, Beijing 100083, China
| | - Chen Fang
- Laboratory of Biomass and Bioprocessing Engineering, College of Engineering, China Agricultural University, Beijing 100083, China
| | - Xiaoxi Sun
- Laboratory of Biomass and Bioprocessing Engineering, College of Engineering, China Agricultural University, Beijing 100083, China
| | - Lujia Han
- Laboratory of Biomass and Bioprocessing Engineering, College of Engineering, China Agricultural University, Beijing 100083, China
| | - Xueqin He
- Laboratory of Biomass and Bioprocessing Engineering, College of Engineering, China Agricultural University, Beijing 100083, China
| | - Guangqun Huang
- Laboratory of Biomass and Bioprocessing Engineering, College of Engineering, China Agricultural University, Beijing 100083, China.
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75
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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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76
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Ren J, Song C, Hou A, Song Y, Zhu X, Cagle GA. Shifts in soil bacterial and archaeal communities during freeze-thaw cycles in a seasonal frozen marsh, Northeast China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 625:782-791. [PMID: 29306166 DOI: 10.1016/j.scitotenv.2017.12.309] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 12/19/2017] [Accepted: 12/27/2017] [Indexed: 06/07/2023]
Abstract
Diurnal freeze-thaw cycles (FTCs) occur in the spring and autumn in boreal wetlands as soil temperatures rise above freezing during the day and fall below freezing at night. A surge in methane emissions from these systems is frequently documented during spring FTCs, accounting for a large portion of annual emissions. In boreal wetlands, methane is produced as a result of syntrophic microbial processes, mediated by a consortium of fermenting bacteria and methanogenic archaea. Further research is needed to determine whether FTCs enhance microbial metabolism related to methane production through the cryogenic decomposition of soil organic matter. Previous studies observed large methane emissions during the spring thawed period in the Sanjiang seasonal frozen marsh of Northeast China. To investigate how FTCs impact the soil microbial community and methanogen abundance and activity, we collected soil cores from the Sanjiang marsh during the FTCs of autumn 2014 and spring 2015. Methanogens were investigated based on expression level of the methyl coenzyme reductase (mcrA) gene, and soil bacterial and archaeal community structures were assessed by 16S rRNA gene sequencing. The results show that a decrease in bacteria and methanogens followed autumns FTCs, whereas an increase in bacteria and methanogens was observed following spring FTCs. The bacterial community structure, including Firmicutes and certain Deltaproteobacteria, was changed following autumn FTCs. Temperature and substrate were the primary factors regulating the abundance and composition of the microbial communities during autumn FTCs, whereas no factors significantly contributing to spring FTCs were identified. Acetoclastic methanogens from order Methanosarcinales were the dominant group at the beginning and end of both the autumn and spring FTCs. Active methanogens were significantly more abundant during the diurnal thawed period, indicating that the increasing number of FTCs predicted to occur with global climate change could potentially promote CH4 emissions in seasonal frozen marshes.
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Affiliation(s)
- Jiusheng Ren
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Changchun Song
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, PR China.
| | - Aixin Hou
- Department of Environmental Sciences, College of the Coast and Environment, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Yanyu Song
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, PR China
| | - Xiaoyan Zhu
- Key Laboratory of Songliao Aquatic Environment, Ministry of Education, Jilin Jianzhu University, Xincheng Street, District 5088, Changchun 130118, PR China
| | - Grace Ann Cagle
- Department of Environmental Sciences, College of the Coast and Environment, Louisiana State University, Baton Rouge, LA 70803, USA
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77
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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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78
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Chen J, Zhang H, Wu X, Shang S, Yan J, Chen Y, Zhang H, Tang X. Characterization of the gut microbiota in the golden takin (Budorcas taxicolor bedfordi). AMB Express 2017; 7:81. [PMID: 28413853 PMCID: PMC5392452 DOI: 10.1186/s13568-017-0374-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 03/21/2017] [Indexed: 02/01/2023] Open
Abstract
The gut microbiota of mammals is a complex ecosystem, which is essential for maintaining gut homeostasis and the host's health. The high throughput sequencing allowed us to gain a deeper insight into the bacterial structure and diversity. In order to improve the health status of the endangered golden takins, we first characterized the fecal microbiota of healthy golden takins using high throughput sequencing of the 16S rRNA genes V3-V4 hypervariable regions. Our results showed that, Firstly, the gut microbiota community comprised 21 phyla, 40 classes, 62 orders, 96 families, and 216 genera. Firmicutes (67.59%) was the most abundant phylum, followed by Bacteroidetes (23.57%) and Proteobacteria (2.37%). Secondly, the golden takin maintained higher richness in spring than in the winter while community diversity and evenness was not significantly different. Thirdly, four female golden takins demonstrated highly similar microbiota and the five golden takin males had relatively highly similar microbiota. All of our results might indicate that the fecal microbiota of golden takins were influenced by the season and the animal's sex. The findings provided theoretical basis regarding the gut microbiota of golden takins and may offer new insights to protect this endangered species.
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79
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Kolinko S, Wu YW, Tachea F, Denzel E, Hiras J, Gabriel R, Bäcker N, Chan LJG, Eichorst SA, Frey D, Chen Q, Azadi P, Adams PD, Pray TR, Tanjore D, Petzold CJ, Gladden JM, Simmons BA, Singer SW. A bacterial pioneer produces cellulase complexes that persist through community succession. Nat Microbiol 2017; 3:99-107. [PMID: 29109478 PMCID: PMC6794216 DOI: 10.1038/s41564-017-0052-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 10/04/2017] [Indexed: 11/16/2022]
Abstract
Cultivation of microbial consortia provides low-complexity communities that can serve as tractable models to understand community dynamics. Time-resolved metagenomics demonstrated that an aerobic cellulolytic consortium cultivated from compost exhibited community dynamics consistent with the definition of an endogenous heterotrophic succession. The genome of the proposed pioneer population, ‘Candidatus Reconcilibacillus cellulovorans’, possessed a gene cluster containing multidomain glycoside hydrolases (GHs). Purification of the soluble cellulase activity from a 300litre cultivation of this consortium revealed that ~70% of the activity arose from the ‘Ca. Reconcilibacillus cellulovorans’ multidomain GHs assembled into cellulase complexes through glycosylation. These remarkably stable complexes have supramolecular structures for enzymatic cellulose hydrolysis that are distinct from cellulosomes. The persistence of these complexes during cultivation indicates that they may be active through multiple cultivations of this consortium and act as public goods that sustain the community. The provision of extracellular GHs as public goods may influence microbial community dynamics in native biomass-deconstructing communities relevant to agriculture, human health and biotechnology. Cultivation of a cellulolytic consortium reveals successional community dynamics and the presence of multidomain glycoside hydrolases assembled into stable complexes distinct from cellulosomes, which are produced by a potential pioneer population.
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Affiliation(s)
- Sebastian Kolinko
- Joint BioEnergy Institute, Emeryville, CA, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yu-Wei Wu
- Joint BioEnergy Institute, Emeryville, CA, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Firehiwot Tachea
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Advanced Biofuels Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
| | - Evelyn Denzel
- Joint BioEnergy Institute, Emeryville, CA, USA.,Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Faculty of Biotechnology, University of Applied Sciences, Mannheim, Germany
| | - Jennifer Hiras
- Joint BioEnergy Institute, Emeryville, CA, USA.,Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Corning Incorporated, Corning, NY, USA
| | - Raphael Gabriel
- Joint BioEnergy Institute, Emeryville, CA, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Institut für Genetik, Technische Universität Braunschweig, Braunschweig, Germany
| | - Nora Bäcker
- Joint BioEnergy Institute, Emeryville, CA, USA.,Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Faculty of Biotechnology, University of Applied Sciences, Mannheim, Germany
| | - Leanne Jade G Chan
- Joint BioEnergy Institute, Emeryville, CA, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Stephanie A Eichorst
- Joint BioEnergy Institute, Emeryville, CA, USA.,Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research network "Chemistry meets Microbiology", University of Vienna, Vienna, Austria
| | - Dario Frey
- Joint BioEnergy Institute, Emeryville, CA, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Faculty of Biotechnology, University of Applied Sciences, Mannheim, Germany
| | - Qiushi Chen
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Paul D Adams
- Joint BioEnergy Institute, Emeryville, CA, USA.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Todd R Pray
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Advanced Biofuels Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
| | - Deepti Tanjore
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Advanced Biofuels Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
| | - Christopher J Petzold
- Joint BioEnergy Institute, Emeryville, CA, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - John M Gladden
- Joint BioEnergy Institute, Emeryville, CA, USA.,Biological and Materials Science Center, Sandia National Laboratories, Livermore, CA, USA
| | - Blake A Simmons
- Joint BioEnergy Institute, Emeryville, CA, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Steven W Singer
- Joint BioEnergy Institute, Emeryville, CA, USA. .,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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80
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Bai Z, Xie H, Kao-Kniffin J, Chen B, Shao P, Liang C. Shifts in microbial trophic strategy explain different temperature sensitivity of CO2 flux under constant and diurnally varying temperature regimes. FEMS Microbiol Ecol 2017; 93:3814241. [PMID: 28499007 DOI: 10.1093/femsec/fix063] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 05/09/2017] [Indexed: 12/31/2022] Open
Abstract
Understanding soil CO2 flux temperature sensitivity (Q10) is critical for predicting ecosystem-level responses to climate change. Yet, the effects of warming on microbial CO2 respiration still remain poorly understood under current Earth system models, partly as a result of thermal acclimation of organic matter decomposition. We conducted a 117-day incubation experiment under constant and diurnally varying temperature treatments based on four forest soils varying in vegetation stand and soil horizon. Our results showed that Q10 was greater under varying than constant temperature regimes. This distinction was most likely attributed to differences in the depletion of available carbon between constant high and varying high-temperature treatments, resulting in significantly higher rates of heterotrophic respiration in the varying high-temperature regime. Based on 16S rRNA gene sequencing data using Illumina, the varying high-temperature regime harbored higher prokaryotic alpha-diversity, was more dominated by the copiotrophic strategists and sustained a distinct community composition, in comparison to the constant-high treatment. We found a tightly coupled relationship between Q10 and microbial trophic guilds: the copiotrophic prokaryotes responded positively with high Q10 values, while the oligotrophs showed a negative response. Effects of vegetation stand and soil horizon consistently supported that the copiotrophic vs oligotrophic strategists determine the thermal sensitivity of CO2 flux. Our observations suggest that incorporating prokaryotic functional traits, such as shifts between copiotrophy and oligotrophy, is fundamental to our understanding of thermal acclimation of microbially mediated soil organic carbon cycling. Inclusion of microbial functional shifts may provide the potential to improve our projections of responses in microbial community and CO2 efflux to a changing environment in forest ecosystems.
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Affiliation(s)
- Zhen Bai
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Hongtu Xie
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Jenny Kao-Kniffin
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Baodong Chen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Pengshuai Shao
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Chao Liang
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
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81
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Zhou X, Zhang Z, Tian L, Li X, Tian C. Microbial communities in peatlands along a chronosequence on the Sanjiang Plain, China. Sci Rep 2017; 7:9567. [PMID: 28852134 PMCID: PMC5575048 DOI: 10.1038/s41598-017-10436-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 08/09/2017] [Indexed: 02/01/2023] Open
Abstract
Microbial communities play crucial roles in the global carbon cycle, particularly in peatland ecosystems under climate change. The peatlands of the Sanjiang Plain could be highly vulnerable to global warming because they are mainly located at the southern limit of northern peatlands. In this study, the alpha diversity and composition of bacterial communities in three different minerotrophic fens along a chronosequence were investigated. We captured a rich microbial community that included many rare operational taxonomic units (OTUs) but was dominated by a few bacterial classes that have frequently been detected in other peatland ecosystems. Notably, a large diversity of methanotrophs affiliated with Alpha- and Gammaproteobacteria was also detected. Bacterial alpha diversity and composition varied as a function of peat depth and its associated physical-chemical properties, such as total carbon, total nitrogen, pH and bulk density. We also found that bacterial community turnover (beta diversity) to be significantly correlated with soil age, whereas bacterial alpha diversity was not.
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Affiliation(s)
- Xue Zhou
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
| | - Zhenqing Zhang
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
| | - Lei Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China.,University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiujun Li
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
| | - Chunjie Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China.
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82
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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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83
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Baldrian P. Forest microbiome: diversity, complexity and dynamics. FEMS Microbiol Rev 2016; 41:109-130. [DOI: 10.1093/femsre/fuw040] [Citation(s) in RCA: 168] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/08/2016] [Indexed: 12/13/2022] Open
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84
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Danilova OV, Belova SE, Gagarinova IV, Dedysh SN. Microbial community composition and methanotroph diversity of a subarctic wetland in Russia. Microbiology (Reading) 2016. [DOI: 10.1134/s0026261716050039] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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85
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Ivanova AA, Wegner CE, Kim Y, Liesack W, Dedysh SN. Identification of microbial populations driving biopolymer degradation in acidic peatlands by metatranscriptomic analysis. Mol Ecol 2016; 25:4818-35. [DOI: 10.1111/mec.13806] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 06/12/2016] [Accepted: 08/11/2016] [Indexed: 11/30/2022]
Affiliation(s)
- Anastasia A. Ivanova
- Winogradsky Institute of Microbiology; Research Center of Biotechnology of the Russian Academy of Sciences; 33, bld. 2 Leninsky Ave. Moscow 119071 Russia
| | - Carl-Eric Wegner
- Max Planck Institute for Terrestrial Microbiology; D-35043 Marburg Germany
| | - Yongkyu Kim
- Max Planck Institute for Terrestrial Microbiology; D-35043 Marburg Germany
| | - Werner Liesack
- Max Planck Institute for Terrestrial Microbiology; D-35043 Marburg Germany
| | - Svetlana N. Dedysh
- Winogradsky Institute of Microbiology; Research Center of Biotechnology of the Russian Academy of Sciences; 33, bld. 2 Leninsky Ave. Moscow 119071 Russia
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86
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Harbison AB, Carson MA, Lamit LJ, Basiliko N, Bräuer SL. A novel isolate and widespread abundance of the candidate alphaproteobacterial order (Ellin 329), in southern Appalachian peatlands. FEMS Microbiol Lett 2016; 363:fnw151. [DOI: 10.1093/femsle/fnw151] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/01/2016] [Indexed: 01/20/2023] Open
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87
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Nikrad MP, Kerkhof LJ, Häggblom MM. The subzero microbiome: microbial activity in frozen and thawing soils. FEMS Microbiol Ecol 2016; 92:fiw081. [PMID: 27106051 DOI: 10.1093/femsec/fiw081] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/17/2016] [Indexed: 01/15/2023] Open
Abstract
Most of the Earth's biosphere is characterized by low temperatures (<5°C) and cold-adapted microorganisms are widespread. These psychrophiles have evolved a complex range of adaptations of all cellular constituents to counteract the potentially deleterious effects of low kinetic energy environments and the freezing of water. Microbial life continues into the subzero temperature range, and this activity contributes to carbon and nitrogen flux in and out of ecosystems, ultimately affecting global processes. Microbial responses to climate warming and, in particular, thawing of frozen soils are not yet well understood, although the threat of microbial contribution to positive feedback of carbon flux is substantial. To date, several studies have examined microbial community dynamics in frozen soils and permafrost due to changing environmental conditions, and some have undertaken the complicated task of characterizing microbial functional groups and how their activity changes with changing conditions, either in situ or by isolating and characterizing macromolecules. With increasing temperature and wetter conditions microbial activity of key microbes and subsequent efflux of greenhouse gases also increase. In this review, we aim to provide an overview of microbial activity in seasonally frozen soils and permafrost. With a more detailed understanding of the microbiological activities in these vulnerable soil ecosystems, we can begin to predict and model future expectations for carbon release and climate change.
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Affiliation(s)
| | - Lee J Kerkhof
- Department of Marine and Coastal Sciences, Rutgers, the State University of New Jersey, New Brunswick, NJ 08901, USA
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88
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Zeng Q, Dong Y, An S. Bacterial Community Responses to Soils along a Latitudinal and Vegetation Gradient on the Loess Plateau, China. PLoS One 2016; 11:e0152894. [PMID: 27045518 PMCID: PMC4821562 DOI: 10.1371/journal.pone.0152894] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 03/21/2016] [Indexed: 11/19/2022] Open
Abstract
Soil bacterial communities play an important role in nutrient recycling and storage in terrestrial ecosystems. Loess soils are one of the most important soil resources for maintaining the stability of vegetation ecosystems and are mainly distributed in northwest China. Estimating the distributions and affecting factors of soil bacterial communities associated with various types of vegetation will inform our understanding of the effect of vegetation restoration and climate change on these processes. In this study, we collected soil samples from 15 sites from north to south on the Loess Plateau of China that represent different ecosystem types and analyzed the distributions of soil bacterial communities by high-throughput 454 pyrosequencing. The results showed that the 142444 sequences were grouped into 36816 operational taxonomic units (OTUs) based on 97% similarity. The results of the analysis showed that the dominant taxonomic phyla observed in all samples were Actinobacteria, Proteobacteria, Chloroflexi, Acidobacteria and Planctomycetes. Actinobacteria and Proteobacteria were the two most abundant groups in all samples. The relative abundance of Actinobacteria increased from 14.73% to 40.22% as the ecosystem changed from forest to sandy, while the relative abundance of Proteobacteria decreased from 35.35% to 21.40%. Actinobacteria and Proteobacteria had significant correlations with mean annual precipitation (MAP), pH, and soil moisture and nutrients. MAP was significantly correlated with soil chemical and physical properties. The relative abundance of Actinobacteria, Proteobacteria and Planctomycetes correlated significantly with MAP, suggesting that MAP was a key factor that affected the soil bacterial community composition. However, along with the MAP gradient, Chloroflexi, Bacteroidetes and Cyanobacteria had narrow ranges that did not significantly vary with the soil and environmental factors. Overall, we conclude that the edaphic properties and/or vegetation types are driving bacterial community composition. MAP was a key factor that affects the composition of the soil bacteria on the Loess Plateau of China.
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Affiliation(s)
- Quanchao Zeng
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, P.R. China
| | - Yanghong Dong
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, P.R. China
| | - Shaoshan An
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, P.R. China
- State Key Laboratory of Soil Erosion and Dry Land Farming on Loess Plateau, Northwest A&F University, Yangling, Shaanxi, P.R. China
- * E-mail:
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89
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Zhou G, Zhang J, Zhang C, Feng Y, Chen L, Yu Z, Xin X, Zhao B. Effects of changes in straw chemical properties and alkaline soils on bacterial communities engaged in straw decomposition at different temperatures. Sci Rep 2016; 6:22186. [PMID: 26916902 PMCID: PMC4768159 DOI: 10.1038/srep22186] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 02/03/2016] [Indexed: 12/30/2022] Open
Abstract
Differences in the composition of a bacterial community engaged in decomposing wheat straw in a fluvo-aquic soil at 15 °C, 25 °C, and 35 °C were identified using barcode pyrosequencing. Functional carbon groups in the decomposing wheat straw were evaluated by 13C-NMR (nuclear magnetic resonance). Actinobacteria and Firmicutes were more abundant, whereas Alphaproteobacteria and Bacteroidetes were less abundant, at higher temperatures during the later stages of decomposition. Differences in the chemical properties of straw accounted for 19.3% of the variation in the community composition, whereas soil properties accounted for more (24.0%) and temperature, for less (7.4%). Carbon content of the soil microbial biomass and nitrogen content of straw were significantly correlated with the abundance of Alphaproteobacteria, Actinobacteria, and Bacteroidetes. The chemical properties of straw, especially the NCH/OCH3, alkyl O-C-O, and O-alkyl functional groups, exercised a significant effect on the composition of the bacterial community at different temperatures during decomposition—results that extend our understanding of bacterial communities associated with the decomposition of straw in agro-ecosystems and of the effects of temperature and chemical properties of the decomposing straw and soil on such communities.
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Affiliation(s)
- Guixiang Zhou
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.,Poyang Lake Eco-economy Research Center, Jiujiang University, Jiujiang 332005, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiabao Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Congzhi Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Youzhi Feng
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Lin Chen
- Institute of Soil and Water Resources and Environmental Science, College of Environmental&Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zhenghong Yu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiuli Xin
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Bingzi Zhao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
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90
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García-Fraile P, Benada O, Cajthaml T, Baldrian P, Lladó S. Terracidiphilus gabretensis gen. nov., sp. nov., an Abundant and Active Forest Soil Acidobacterium Important in Organic Matter Transformation. Appl Environ Microbiol 2016; 82:560-9. [PMID: 26546425 PMCID: PMC4711116 DOI: 10.1128/aem.03353-15] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 11/02/2015] [Indexed: 01/22/2023] Open
Abstract
Understanding the activity of bacteria in coniferous forests is highly important, due to the role of these environments as a global carbon sink. In a study of the microbial biodiversity of montane coniferous forest soil in the Bohemian Forest National Park (Czech Republic), we succeeded in isolating bacterial strain S55(T), which belongs to one of the most abundant operational taxonomic units (OTUs) in active bacterial populations, according to the analysis of RNA-derived 16S rRNA amplicons. The 16S rRNA gene sequence analysis showed that the species most closely related to strain S55(T) include Bryocella elongata SN10(T) (95.4% identity), Acidicapsa ligni WH120(T) (95.2% identity), and Telmatobacter bradus TPB6017(T) (95.0% identity), revealing that strain S55(T) should be classified within the phylum Acidobacteria, subdivision 1. Strain S55(T) is a rod-like bacterium that grows at acidic pH (3 to 6). Its phylogenetic, genotypic, phenotypic, and chemotaxonomic characteristics indicate that strain S55(T) corresponds to a new genus within the phylum Acidobacteria; thus, we propose the name Terracidiphilus gabretensis gen. nov., sp. nov. (strain S55(T) = NBRC 111238(T) = CECT 8791(T)). This strain produces extracellular enzymes implicated in the degradation of plant-derived biopolymers. Moreover, analysis of the genome sequence of strain S55(T) also reveals the presence of enzymatic machinery required for organic matter decomposition. Soil metatranscriptomic analyses found 132 genes from strain S55(T) being expressed in the forest soil, especially during winter. Our results suggest an important contribution of T. gabretensis S55(T) in the carbon cycle in the Picea abies coniferous forest.
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Affiliation(s)
- Paula García-Fraile
- Institute of Microbiology ASCR, Laboratory of Fungal Genetics and Metabolism, Prague, Czech Republic
| | - Oldrich Benada
- Institute of Microbiology ASCR, Laboratory of Molecular Structure Characterization, Prague, Czech Republic
| | - Tomáš Cajthaml
- Institute of Microbiology ASCR, Laboratory of Environmental Biotechnology, Prague, Czech Republic
| | - Petr Baldrian
- Institute of Microbiology ASCR, Laboratory of Environmental Microbiology, Prague, Czech Republic
| | - Salvador Lladó
- Institute of Microbiology ASCR, Laboratory of Environmental Microbiology, Prague, Czech Republic
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91
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Ballaud F, Dufresne A, Francez AJ, Colombet J, Sime-Ngando T, Quaiser A. Dynamics of Viral Abundance and Diversity in a Sphagnum-Dominated Peatland: Temporal Fluctuations Prevail Over Habitat. Front Microbiol 2016; 6:1494. [PMID: 26779149 PMCID: PMC4701944 DOI: 10.3389/fmicb.2015.01494] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 12/11/2015] [Indexed: 11/23/2022] Open
Abstract
Viruses impact microbial activity and carbon cycling in various environments, but their diversity and ecological importance in Sphagnum-peatlands are unknown. Abundances of viral particles and prokaryotes were monitored bi-monthly at a fen and a bog at two different layers of the peat surface. Viral particle abundance ranged from 1.7 x 106 to 5.6 x 108 particles mL-1, and did not differ between fen and bog but showed seasonal fluctuations. These fluctuations were positively correlated with prokaryote abundance and dissolved organic carbon, and negatively correlated with water-table height and dissolved oxygen. Using shotgun metagenomics we observed a shift in viral diversity between winter/spring and summer/autumn, indicating a seasonal succession of viral communities, mainly driven by weather-related environmental changes. Based on the seasonal asynchrony between viral and microbial diversity, we hypothesize a seasonal shift in the active microbial communities associated with a shift from lysogenic to lytic lifestyles. Our results suggest that temporal variations of environmental conditions rather than current habitat differences control the dynamics of virus-host interactions in Sphagnum-dominated peatlands.
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Affiliation(s)
- Flore Ballaud
- UMR CNRS 6553 ECOBIO, Université de Rennes 1 Rennes, France
| | | | | | - Jonathan Colombet
- Université Clermont Auvergne, Université Blaise PascalClermont-Ferrand, France; CNRS, UMR 6023, Laboratoire Microorganismes: Génome et EnvironnementAubière, France
| | - Télesphore Sime-Ngando
- Université Clermont Auvergne, Université Blaise PascalClermont-Ferrand, France; CNRS, UMR 6023, Laboratoire Microorganismes: Génome et EnvironnementAubière, France
| | - Achim Quaiser
- UMR CNRS 6553 ECOBIO, Université de Rennes 1 Rennes, France
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92
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Discovery of a novel methanogen prevalent in thawing permafrost. Nat Commun 2015; 5:3212. [PMID: 24526077 DOI: 10.1038/ncomms4212] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 01/07/2014] [Indexed: 12/21/2022] Open
Abstract
Thawing permafrost promotes microbial degradation of cryo-sequestered and new carbon leading to the biogenic production of methane, creating a positive feedback to climate change. Here we determine microbial community composition along a permafrost thaw gradient in northern Sweden. Partially thawed sites were frequently dominated by a single archaeal phylotype, Candidatus 'Methanoflorens stordalenmirensis' gen. nov. sp. nov., belonging to the uncultivated lineage 'Rice Cluster II' (Candidatus 'Methanoflorentaceae' fam. nov.). Metagenomic sequencing led to the recovery of its near-complete genome, revealing the genes necessary for hydrogenotrophic methanogenesis. These genes are highly expressed and methane carbon isotope data are consistent with hydrogenotrophic production of methane in the partially thawed site. In addition to permafrost wetlands, 'Methanoflorentaceae' are widespread in high methane-flux habitats suggesting that this lineage is both prevalent and a major contributor to global methane production. In thawing permafrost, Candidatus 'M. stordalenmirensis' appears to be a key mediator of methane-based positive feedback to climate warming.
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93
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Moore EK, Villanueva L, Hopmans EC, Rijpstra WIC, Mets A, Dedysh SN, Sinninghe Damsté JS. Abundant Trimethylornithine Lipids and Specific Gene Sequences Are Indicative of Planctomycete Importance at the Oxic/Anoxic Interface in Sphagnum-Dominated Northern Wetlands. Appl Environ Microbiol 2015; 81:6333-44. [PMID: 26150465 PMCID: PMC4542221 DOI: 10.1128/aem.00324-15] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 06/30/2015] [Indexed: 12/19/2022] Open
Abstract
Northern wetlands make up a substantial terrestrial carbon sink and are often dominated by decay-resistant Sphagnum mosses. Recent studies have shown that planctomycetes appear to be involved in degradation of Sphagnum-derived debris. Novel trimethylornithine (TMO) lipids have recently been characterized as abundant lipids in various Sphagnum wetland planctomycete isolates, but their occurrence in the environment has not yet been confirmed. We applied a combined intact polar lipid (IPL) and molecular analysis of peat cores collected from two northern wetlands (Saxnäs Mosse [Sweden] and Obukhovskoye [Russia]) in order to investigate the preferred niche and abundance of TMO-producing planctomycetes. TMOs were present throughout the profiles of Sphagnum bogs, but their concentration peaked at the oxic/anoxic interface, which coincided with a maximum abundance of planctomycete-specific 16S rRNA gene sequences. The sequences detected at the oxic/anoxic interface were affiliated with the Isosphaera group, while sequences present in the anoxic peat layers were related to an uncultured planctomycete group. Pyrosequencing-based analysis identified Planctomycetes as the major bacterial group at the oxic/anoxic interface at the Obukhovskoye peat (54% of total 16S rRNA gene sequence reads), followed by Acidobacteria (19% reads), while in the Saxnäs Mosse peat, Acidobacteria were dominant (46%), and Planctomycetes contributed to 6% of the total reads. The detection of abundant TMO lipids in planctomycetes isolated from peat bogs and the lack of TMO production by cultures of acidobacteria suggest that planctomycetes are the producers of TMOs in peat bogs. The higher accumulation of TMOs at the oxic/anoxic interface and the change in the planctomycete community with depth suggest that these IPLs could be synthesized as a response to changing redox conditions at the oxic/anoxic interface.
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Affiliation(s)
- Eli K Moore
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Organic Biogeochemistry, Texel, The Netherlands
| | - Laura Villanueva
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Organic Biogeochemistry, Texel, The Netherlands
| | - Ellen C Hopmans
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Organic Biogeochemistry, Texel, The Netherlands
| | - W Irene C Rijpstra
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Organic Biogeochemistry, Texel, The Netherlands
| | - Anchelique Mets
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Organic Biogeochemistry, Texel, The Netherlands
| | - Svetlana N Dedysh
- S. N. Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
| | - Jaap S Sinninghe Damsté
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Organic Biogeochemistry, Texel, The Netherlands Utrecht University, Faculty of Geosciences, Utrecht, The Netherlands
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94
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Quiroga MV, Valverde A, Mataloni G, Cowan D. Understanding diversity patterns in bacterioplankton communities from a sub-Antarctic peatland. ENVIRONMENTAL MICROBIOLOGY REPORTS 2015; 7:547-553. [PMID: 25727763 DOI: 10.1111/1758-2229.12287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 02/22/2015] [Indexed: 06/04/2023]
Abstract
Bacterioplankton communities inhabiting peatlands have the potential to influence local ecosystem functions. However, most microbial ecology research in such wetlands has been done in ecosystems (mostly peat soils) of the Northern Hemisphere, and very little is known of the factors that drive bacterial community assembly in other regions of the world. In this study, we used high-throughput sequencing to analyse the structure of the bacterial communities in five pools located in a sub-Antarctic peat bog (Tierra del Fuego, Argentina), and tested for relationships between bacterial communities and environmental conditions. Bacterioplankton communities in peat bog pools were diverse and dominated by members of the Proteobacteria, Actinobacteria, Bacteroidetes and Verrucomicrobia. Community structure was largely explained by differences in hydrological connectivity, pH and nutrient status (ombrotrophic versus minerotrophic pools). Bacterioplankton communities in ombrotrophic pools showed phylogenetic clustering, suggesting a dominant role of deterministic processes in shaping these assemblages. These correlations between habitat characteristics and bacterial diversity patterns provide new insights into the factors regulating microbial populations in peatland ecosystems.
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Affiliation(s)
- María Victoria Quiroga
- Instituto de Investigación e Ingeniería Ambiental (3iA), Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - Angel Valverde
- Department of Genetics, Centre for Microbial Ecology and Genomics (CMEG), Genomics Research Institute (GRI), University of Pretoria, Pretoria, South Africa
| | - Gabriela Mataloni
- Instituto de Investigación e Ingeniería Ambiental (3iA), Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - Don Cowan
- Department of Genetics, Centre for Microbial Ecology and Genomics (CMEG), Genomics Research Institute (GRI), University of Pretoria, Pretoria, South Africa
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95
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Urbanová Z, Bárta J. Microbial community composition and in silico predicted metabolic potential reflect biogeochemical gradients between distinct peatland types. FEMS Microbiol Ecol 2014; 90:633-46. [PMID: 25195805 DOI: 10.1111/1574-6941.12422] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 08/21/2014] [Accepted: 08/31/2014] [Indexed: 11/30/2022] Open
Abstract
It is not well understood how the ecological status and microbial community composition of spruce swamp forests (SSF) relate to those found in bogs and fens. To clarify this, we investigated biogeochemical parameters and microbial community composition in a bog, a fen and two SSF using high throughput barcoded sequencing of the small ribosomal subunit (SSU) variable region V4. The results demonstrated that the microbial community of SSF is positioned between those of bogs and fens, and this was confirmed by in silico predicted metabolic potentials. This corresponds well with the position of SSF on the trophic gradient and reflects distinct responses of microbial communities to environmental variables. Species richness and microbial diversity increased significantly from bog to fen, with SSF in between, reflecting the variation in pH, nutrient availability and peat decomposability. The archaeal community, dominated by hydrogenotrophic methanogens, was more similar in SSF and the bog compared with the fen. The composition of the bacterial community of SSF was intermediate between those of bog and fen. However, the production of CO2 (an indicator of peat decomposability) did not differ between SSF and bog, suggesting the limiting effect of low pH and poor litter quality on the functioning of the bacterial community in SSF. These results help to clarify the transitional position of SSF between bogs and fens and showed the strong effect of environmental conditions on microbial community composition and functioning.
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Affiliation(s)
- Zuzana Urbanová
- Department of Ecosystem Biology, University of South Bohemia in České Budějovice, České Budějovice, Czech Republic
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96
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Kulichevskaya IS, Suzina NE, Rijpstra WIC, Damsté JSS, Dedysh SN. Paludibaculum fermentans gen. nov., sp. nov., a facultative anaerobe capable of dissimilatory iron reduction from subdivision 3 of the Acidobacteria. Int J Syst Evol Microbiol 2014; 64:2857-2864. [DOI: 10.1099/ijs.0.066175-0] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A facultatively anaerobic, non-pigmented, non-spore-forming bacterium was isolated from a littoral wetland of a boreal lake located on Valaam Island, northern Russia, and designated strain P105T. Cells of this isolate were Gram-negative, non-motile rods coated by S-layers with p2 lattice symmetry. Sugars were the preferred growth substrates. Under anoxic conditions, strain P105T was capable of fermentation and dissimilatory Fe(III) reduction. End products of fermentation were acetate, propionate and H2. Strain P105T was a mildly acidophilic, mesophilic organism, capable of growth at pH 4.0–7.2 (optimum pH 5.5–6.0) and at 4–35 °C (optimum at 20–28 °C). The major fatty acids were iso-C15 : 0 and C16 : 1ω7c; the cells also contained significant amounts of 13,16-dimethyl octacosanedioic acid (isodiabolic acid). The major polar lipids were phosphocholine and phosphoethanolamine; the quinone was MK-8. The G+C content of the DNA was 60.5 mol%. 16S rRNA gene sequence analysis showed that strain P105T belongs to subdivision 3 of the
Acidobacteria
and is only distantly related (90 % sequence similarity) to the only currently characterized member of this subdivision,
Bryobacter aggregatus
. The novel isolate differs from
Bryobacter aggregatus
in its cell morphology and ability to grow under anoxic conditions and in the presence of iron- and nitrate-reducing capabilities as well as quinone and polar lipid compositions. These differences suggest that strain P105T represents a novel genus and species, for which the name Paludibaculum fermentans gen. nov., sp. nov., is proposed. The type strain of Paludibaculum fermentans is P105T ( = DSM 26340T = VKM B-2878T).
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Affiliation(s)
- Irina S. Kulichevskaya
- S. N. Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letya Octyabrya 7/2, Moscow 117312, Russia
| | - Natalia E. Suzina
- G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow region 142292, Russia
| | - W. Irene C. Rijpstra
- Royal Netherlands Institute for Sea Research, Department of Marine Organic Biogeochemistry, PO Box 59, 1790 AB Den Burg, The Netherlands
| | - Jaap S. Sinninghe Damsté
- Royal Netherlands Institute for Sea Research, Department of Marine Organic Biogeochemistry, PO Box 59, 1790 AB Den Burg, The Netherlands
| | - Svetlana N. Dedysh
- S. N. Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letya Octyabrya 7/2, Moscow 117312, Russia
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97
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Schmidt O, Horn MA, Kolb S, Drake HL. Temperature impacts differentially on the methanogenic food web of cellulose-supplemented peatland soil. Environ Microbiol 2014; 17:720-34. [PMID: 24813682 DOI: 10.1111/1462-2920.12507] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 05/07/2014] [Indexed: 11/29/2022]
Abstract
The impact of temperature on the largely unresolved intermediary ecosystem metabolism and associated unknown microbiota that link cellulose degradation and methane production in soils of a moderately acidic (pH 4.5) fen was investigated. Supplemental [(13) C]cellulose stimulated the accumulation of propionate, acetate and carbon dioxide as well as initial methane production in anoxic peat soil slurries at 15°C and 5°C. Accumulation of organic acids at 15°C was twice as fast as that at 5°C. 16S rRNA [(13) C]cellulose stable isotope probing identified novel unclassified Bacteria (79% identity to the next cultured relative Fibrobacter succinogenes), unclassified Bacteroidetes (89% identity to Prolixibacter bellariivorans), Porphyromonadaceae, Acidobacteriaceae and Ruminococcaceae as main anaerobic degraders of cellulose-derived carbon at both 15°C and 5°C. Holophagaceae and Spirochaetaceae were more abundant at 15°C. Clostridiaceae dominated the degradation of cellulose-derived carbon only at 5°C. Methanosarcina was the dominant methanogenic taxa at both 15°C and 5°C. Relative abundance of Methanocella increased at 15°C whereas that of Methanoregula and Methanosaeta increased at 5°C. Thaumarchaeota closely related to Nitrosotalea (presently not known to grow anaerobically) were abundant at 5°C but absent at 15°C indicating that Nitrosotalea sp. might be capable of anaerobic growth at low temperatures in peat.
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Affiliation(s)
- Oliver Schmidt
- Department of Ecological Microbiology, University of Bayreuth, Bayreuth, 95440, Germany
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98
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Etto RM, Cruz LM, da Conceição Jesus E, Galvão CW, Galvão F, de Souza EM, de Oliveira Pedrosa F, Reynaud Steffens MB. Seasonal changes in dominant bacterial taxa from acidic peatlands of the Atlantic Rain Forest. Res Microbiol 2014; 165:517-25. [PMID: 24893336 DOI: 10.1016/j.resmic.2014.05.036] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 05/22/2014] [Indexed: 11/25/2022]
Abstract
The acidic peatlands of southern Brazil are essential for maintenance of the Atlantic Rain Forest, one of the 25 hot-spots of biodiversity in the world. While these ecosystems are closely linked to conservation issues, their microbial community ecology and composition remain unknown. In this work, histosol samples were collected from three acidic peatland regions during dry and rainy seasons and their chemical and microbial characteristics were evaluated. Culturing and culture-independent approaches based on SSU rRNA gene pyrosequencing were used to survey the bacterial community and to identify environmental factors affecting the biodiversity and microbial metabolic potential of the Brazilian peatlands. All acidic peatlands were dominated by the Acidobacteria phylum (56-22%) followed by Proteobacteria (28-12%). The OTU richness of these phyla and the abundance of their Gp1, Gp2, Gp3, Gp13, Rhodospirillales and Caulobacteriales members varied according to the period of collection and significantly correlated with the rainy season. However, despite changes in acidobacterial and proteobacterial communities, rainfall did not affect the microbial metabolic potential of the southern Brazilian Atlantic Rain Forest peatlands, as judged by the metabolic capabilities of the microbial community.
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Affiliation(s)
- Rafael Mazer Etto
- Department of Chemistry, Universidade Estadual de Ponta Grossa, CEP 84030-900, Ponta Grossa, Paraná, Brazil.
| | - Leonardo Magalhães Cruz
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Caixa Postal 19046, CEP 81531-990, Curitiba, Paraná, Brazil.
| | | | - Carolina Weigert Galvão
- Department of Structural and Molecular Biology and Genetics, Universidade Estadual de Ponta Grossa, CEP 84030-900, Ponta Grossa, Paraná, Brazil.
| | - Franklin Galvão
- Department of Forest Sciences, Universidade Federal do Paraná, CEP 80210-170, Curitiba, Paraná, Brazil.
| | - Emanuel Maltempi de Souza
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Caixa Postal 19046, CEP 81531-990, Curitiba, Paraná, Brazil.
| | - Fábio de Oliveira Pedrosa
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Caixa Postal 19046, CEP 81531-990, Curitiba, Paraná, Brazil.
| | - Maria Berenice Reynaud Steffens
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Caixa Postal 19046, CEP 81531-990, Curitiba, Paraná, Brazil.
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99
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Kim M, Kim WS, Tripathi BM, Adams J. Distinct bacterial communities dominate tropical and temperate zone leaf litter. MICROBIAL ECOLOGY 2014; 67:837-848. [PMID: 24549745 DOI: 10.1007/s00248-014-0380-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 01/30/2014] [Indexed: 06/03/2023]
Abstract
Little is known of the bacterial community of tropical rainforest leaf litter and how it might differ from temperate forest leaf litter and from the soils underneath. We sampled leaf litter in a similarly advanced stage of decay, and for comparison, we also sampled the surface layer of soil, at three tropical forest sites in Malaysia and four temperate forest sites in South Korea. Illumina sequencing targeting partial bacterial 16S ribosomal ribonucleic acid (rRNA) gene revealed that the bacterial community composition of both temperate and tropical litter is quite distinct from the soils underneath. Litter in both temperate and tropical forest was dominated by Proteobacteria and Actinobacteria, while soil is dominated by Acidobacteria and, to a lesser extent, Proteobacteria. However, bacterial communities of temperate and tropical litter clustered separately from one another on an ordination. The soil bacterial community structures were also distinctive to each climatic zone, suggesting that there must be a climate-specific biogeographical pattern in bacterial community composition. The differences were also found in the level of diversity. The temperate litter has a higher operational taxonomic unit (OTU) diversity than the tropical litter, paralleling the trend in soil diversity. Overall, it is striking that the difference in community composition between the leaf litter and the soil a few centimeters underneath is about the same as that between leaf litter in tropical and temperate climates, thousands of kilometers apart. However, one substantial difference was that the leaf litter of two tropical forest sites, Meranti and Forest Research Institute Malaysia (FRIM), was overwhelmingly dominated by the single genus Burkholderia, at 37 and 23 % of reads, respectively. The 454 sequencing result showed that most Burkholderia species in tropical leaf litter belong to nonpathogenic "plant beneficial" lineages. The differences from the temperate zone in the bacterial community of tropical forest litter may be partly a product of its differing chemistry, although the unvarying climate might also play a role, as might interactions with other organisms such as fungi. The single genus Burkholderia may be seen as potentially playing a major role in decomposition and nutrient cycling in tropical forests, but apparently not in temperate forests.
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Affiliation(s)
- Mincheol Kim
- School of Biological Sciences, Seoul National University, 599 Gwanak-ro, Gwanak-gu, Seoul, 151-747, Republic of Korea
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100
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Microbial community stratification linked to utilization of carbohydrates and phosphorus limitation in a boreal peatland at Marcell Experimental Forest, Minnesota, USA. Appl Environ Microbiol 2014; 80:3518-30. [PMID: 24682300 DOI: 10.1128/aem.00205-14] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This study investigated the abundance, distribution, and composition of microbial communities at the watershed scale in a boreal peatland within the Marcell Experimental Forest (MEF), Minnesota, USA. Through a close coupling of next-generation sequencing, biogeochemistry, and advanced analytical chemistry, a biogeochemical hot spot was revealed in the mesotelm (30- to 50-cm depth) as a pronounced shift in microbial community composition in parallel with elevated peat decomposition. The relative abundance of Acidobacteria and the Syntrophobacteraceae, including known hydrocarbon-utilizing genera, was positively correlated with carbohydrate and organic acid content, showing a maximum in the mesotelm. The abundance of Archaea (primarily crenarchaeal groups 1.1c and 1.3) increased with depth, reaching up to 60% of total small-subunit (SSU) rRNA gene sequences in the deep peat below the 75-cm depth. Stable isotope geochemistry and potential rates of methane production paralleled vertical changes in methanogen community composition to indicate a predominance of acetoclastic methanogenesis mediated by the Methanosarcinales in the mesotelm, while hydrogen-utilizing methanogens predominated in the deeper catotelm. RNA-derived pyrosequence libraries corroborated DNA sequence data to indicate that the above-mentioned microbial groups are metabolically active in the mid-depth zone. Fungi showed a maximum in rRNA gene abundance above the 30-cm depth, which comprised only an average of 0.1% of total bacterial and archaeal rRNA gene abundance, indicating prokaryotic dominance. Ratios of C to P enzyme activities approached 0.5 at the acrotelm and catotelm, indicating phosphorus limitation. In contrast, P limitation pressure appeared to be relieved in the mesotelm, likely due to P solubilization by microbial production of organic acids and C-P lyases. Based on path analysis and the modeling of community spatial turnover, we hypothesize that P limitation outweighs N limitation at MEF, and microbial communities are structured by the dominant shrub, Chamaedaphne calyculata, which may act as a carbon source for major consumers in the peatland.
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