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Nshimiyimana JB, Zhao K, Wang W, Kong W. Diazotrophic abundance and community structure associated with three meadow plants on the Qinghai-Tibet Plateau. Front Microbiol 2024; 14:1292860. [PMID: 38260880 PMCID: PMC10801153 DOI: 10.3389/fmicb.2023.1292860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 12/20/2023] [Indexed: 01/24/2024] Open
Abstract
Symbiotic diazotrophs form associations with legumes and substantially fix nitrogen into soils. However, grasslands on the Qinghai-Tibet Plateau are dominated by non-legume plants, such as Kobresia tibetica. Herein, we investigated the diazotrophic abundance, composition, and community structure in the soils and roots of three plants, non-legume K. tibetica and Kobresia humilis and the legume Oxytropis ochrocephala, using molecular methods targeting nifH gene. Diazotrophs were abundantly observed in both bulk and rhizosphere soils, as well as in roots of all three plants, but their abundance varied with plant type and soil. In both bulk and rhizosphere soils, K. tibetica showed the highest diazotroph abundance, whereas K. humilis had the lowest. In roots, O. ochrocephala and K. humilis showed the highest and the lowest diazotroph abundance, respectively. The bulk and rhizosphere soils exhibited similar diazotrophic community structure in both O. ochrocephala and K. tibetica, but were substantially distinct from the roots in both plants. Interestingly, the root diazotrophic community structures in legume O. ochrocephala and non-legume K. tibetica were similar. Diazotrophs in bulk and rhizosphere soils were more diverse than those in the roots of three plants. Rhizosphere soils of K. humilis were dominated by Actinobacteria, while rhizosphere soils and roots of K. tibetica were dominated by Verrumicrobia and Proteobacteria. The O. ochrocephala root diazotrophs were dominated by Alphaproteobacteria. These findings indicate that free-living diazotrophs abundantly and diversely occur in grassland soils dominated by non-legume plants, suggesting that these diazotrophs may play important roles in fixing nitrogen into soils on the plateau.
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Affiliation(s)
- Jean Bosco Nshimiyimana
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
- Department of Life and Geography Sciences, Qinghai Normal University, Xining, China
| | - Kang Zhao
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
- Department of Life and Geography Sciences, Qinghai Normal University, Xining, China
| | - Wenying Wang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Biodiversity Formation Mechanism and Comprehensive Utilization in Qinghai Tibet Plateau, Xining, China
| | - Weidong Kong
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
- Department of Life and Geography Sciences, Qinghai Normal University, Xining, China
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Zhao K, Kong W, Khan A, Liu J, Guo G, Muhanmmad S, Zhang X, Dong X. Elevational diversity and distribution of ammonia-oxidizing archaea community in meadow soils on the Tibetan Plateau. Appl Microbiol Biotechnol 2017; 101:7065-7074. [PMID: 28776097 DOI: 10.1007/s00253-017-8435-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 07/12/2017] [Accepted: 07/19/2017] [Indexed: 10/19/2022]
Abstract
Unraveling elevational diversity patterns of plants and animals has long been attracting scientific interests. However, whether soil microorganisms exhibit similar elevational patterns remains largely less explored, especially for functional microbial communities, such as ammonia oxidizers. Here, we investigated the diversity and distribution pattern of ammonia-oxidizing archaea (AOA) in meadow soils along an elevation gradient from 4400 m to the grassline at 5100 m on the Tibetan Plateau using terminal restriction fragment length polymorphism (T-RFLP) and sequencing methods by targeting amoA gene. Increasing elevations led to lower soil temperature and pH, but higher nutrients and water content. The results showed that AOA diversity and evenness monotonically increased with elevation, while richness was relatively stable. The increase of diversity and evenness was attributed to the growth inhibition of warm-adapted AOA phylotypes by lower temperature and the growth facilitation of cold-adapted AOA phylotypes by richer nutrients at higher elevations. Low temperature thus played an important role in the AOA growth and niche separation. The AOA community variation was explained by the combined effect of all soil properties (32.6%), and 8.1% of the total variation was individually explained by soil pH. The total AOA abundance decreased, whereas soil potential nitrification rate (PNR) increased with increasing elevations. Soil PNR positively correlated with the abundance of cold-adapted AOA phylotypes. Our findings suggest that low temperature plays an important role in AOA elevational diversity pattern and niche separation, rising the negative effects of warming on AOA diversity and soil nitrification process in the Tibetan region.
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Affiliation(s)
- Kang Zhao
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Building 3, Courtyard 16, Lincui Road, Chaoyang District, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Weidong Kong
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Building 3, Courtyard 16, Lincui Road, Chaoyang District, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100101, China.
| | - Ajmal Khan
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Building 3, Courtyard 16, Lincui Road, Chaoyang District, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Jinbo Liu
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Building 3, Courtyard 16, Lincui Road, Chaoyang District, Beijing, 100101, China
| | - Guangxia Guo
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Building 3, Courtyard 16, Lincui Road, Chaoyang District, Beijing, 100101, China
| | - Said Muhanmmad
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Building 3, Courtyard 16, Lincui Road, Chaoyang District, Beijing, 100101, China
| | - Xianzhou Zhang
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaobin Dong
- State Key Laboratory of Earth Surface Processes and Resource Ecology, College of Resources Science and Technology, Beijing Normal University, Beijing, 100875, China
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Benzene Degradation by a Variovorax Species within a Coal Tar-Contaminated Groundwater Microbial Community. Appl Environ Microbiol 2017; 83:AEM.02658-16. [PMID: 27913419 DOI: 10.1128/aem.02658-16] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 11/25/2016] [Indexed: 11/20/2022] Open
Abstract
Investigations of environmental microbial communities are crucial for the discovery of populations capable of degrading hazardous compounds and may lead to improved bioremediation strategies. The goal of this study was to identify microorganisms responsible for aerobic benzene degradation in coal tar-contaminated groundwater. Benzene degradation was monitored in laboratory incubations of well waters using gas chromatography mass spectrometry (GC-MS). Stable isotope probing (SIP) experiments using [13C]benzene enabled us to obtain 13C-labled community DNA. From this, 16S rRNA clone libraries identified Gammaproteobacteria and Betaproteobacteria as the active benzene-metabolizing microbial populations. Subsequent cultivation experiments yielded nine bacterial isolates that grew in the presence of benzene; five were confirmed in laboratory cultures to grow on benzene. The isolated benzene-degrading organisms were genotypically similar (>97% 16S rRNA gene nucleotide identities) to the organisms identified in SIP experiments. One isolate, Variovorax MAK3, was further investigated for the expression of a putative aromatic ring-hydroxylating dioxygenase (RHD) hypothesized to be involved in benzene degradation. Microcosm experiments using Variovorax MAK3 revealed a 10-fold increase in RHD (Vapar_5383) expression, establishing a link between this gene and benzene degradation. Furthermore, the addition of Variovorax MAK3 to microcosms prepared from site waters accelerated community benzene degradation and correspondingly increased RHD gene expression. In microcosms using uninoculated groundwater, quantitative (q)PCR assays (with 16S rRNA and RDH genes) showed that Variovorax was present and responsive to added benzene. These data demonstrate how the convergence of cultivation-dependent and -independent techniques can boost understandings of active populations and functional genes in complex benzene-degrading microbial communities. IMPORTANCE Benzene is a human carcinogen whose presence in contaminated groundwater drives environmental cleanup efforts. Although the aerobic biodegradation of benzene has long been established, knowledge of the identity of the microorganisms in complex naturally occurring microbial communities responsible for benzene biodegradation has evaded scientific inquiry for many decades. Here, we applied a molecular biology technique known as stable isotope probing (SIP) to the microbial communities residing in contaminated groundwater samples to identify the community members active in benzene biodegradation. We complemented this approach by isolating and growing in the laboratory a bacterium representative of the bacteria found using SIP. Further characterization of the isolated bacterium enabled us to track the expression of a key gene that attacks benzene both in pure cultures of the bacterium and in the naturally occurring groundwater microbial community. This work advances information regarding the documentation of microbial processes, especially the populations and genes that contribute to bioremediation.
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Liu J, Kong W, Zhang G, Khan A, Guo G, Zhu C, Wei X, Kang S, Morgan-Kiss RM. Diversity and succession of autotrophic microbial community in high-elevation soils along deglaciation chronosequence. FEMS Microbiol Ecol 2016; 92:fiw160. [PMID: 27465079 DOI: 10.1093/femsec/fiw160] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/24/2016] [Indexed: 11/12/2022] Open
Abstract
Global warming has resulted in substantial glacier retreats in high-elevation areas, exposing deglaciated soils to harsh environmental conditions. Autotrophic microbes are pioneering colonizers in the deglaciated soils and provide nutrients to the extreme ecosystem devoid of vegetation. However, autotrophic communities remain less studied in deglaciated soils. We explored the diversity and succession of the cbbL gene encoding the large subunit of form I RubisCO, a key CO2-fixing enzyme, using molecular methods in deglaciated soils along a 10-year deglaciation chronosequence on the Tibetan Plateau. Our results demonstrated that the abundance of all types of form I cbbL (IA/B, IC and ID) rapidly increased in young soils (0-2.5 years old) and kept stable in old soils. Soil total organic carbon (TOC) and total nitrogen (TN) gradually increased along the chronosequence and both demonstrated positive correlations with the abundance of bacteria and autotrophs, indicating that soil TOC and TN originated from autotrophs. Form IA/B autotrophs, affiliated with cyanobacteria, exhibited a substantially higher abundance than IC and ID. Cyanobacterial diversity and evenness increased in young soils (<6 years old) and then remained stable. Our findings suggest that cyabobacteria play an important role in accumulating TOC and TN in the deglaciated soils.
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Affiliation(s)
- Jinbo Liu
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Building 3, Courtyard 16, Lincui Road, Chaoyang District, Beijing 100101, China
| | - Weidong Kong
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Building 3, Courtyard 16, Lincui Road, Chaoyang District, Beijing 100101, China
| | - Guoshuai Zhang
- Key Laboratory of Tibetan Environmental Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Building 3, Courtyard 16, Lincui Road, Chaoyang District, Beijing 100101, China
| | - Ajmal Khan
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Building 3, Courtyard 16, Lincui Road, Chaoyang District, Beijing 100101, China
| | - Guangxia Guo
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Building 3, Courtyard 16, Lincui Road, Chaoyang District, Beijing 100101, China
| | - Chunmao Zhu
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Building 3, Courtyard 16, Lincui Road, Chaoyang District, Beijing 100101, China
| | - Xiaojie Wei
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Building 3, Courtyard 16, Lincui Road, Chaoyang District, Beijing 100101, China
| | - Shichang Kang
- State Key Laboratory of Cryospheric Sciences, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou 730000, China Center for Excellence in Tibetan Plateau Earth Sciences, CAS, Beijing 100101, China
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Pritchard RE, Balish MF. Mycoplasma iowae: relationships among oxygen, virulence, and protection from oxidative stress. Vet Res 2015; 46:36. [PMID: 25880161 PMCID: PMC4367981 DOI: 10.1186/s13567-015-0170-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 03/05/2015] [Indexed: 12/20/2022] Open
Abstract
The poultry-associated bacterium Mycoplasma iowae colonizes multiple sites in embryos, with disease or death resulting. Although M. iowae accumulates in the intestinal tract, it does not cause disease at that site, but rather only in tissues that are exposed to atmospheric O2. The activity of M. iowae catalase, encoded by katE, is capable of rapid removal of damaging H2O2 from solution, and katE confers a substantial reduction in the amount of H2O2 produced by Mycoplasma gallisepticum katE transformants in the presence of glycerol. As catalase-producing bacteria are often beneficial to hosts with inflammatory bowel disease, we explored whether M. iowae was exclusively protective against H2O2-producing bacteria in a Caenorhabditis elegans model, whether its protectiveness changed in response to O2 levels, and whether expression of genes involved in H2O2 metabolism and virulence changed in response to O2 levels. We observed that M. iowae was in fact protective against H2O2-producing Streptococcus pneumoniae, but not HCN-producing Pseudomonas aeruginosa, and that M. iowae cells grown in 1% O2 promoted survival of C. elegans to a greater extent than M. iowae cells grown in atmospheric O2. Transcript levels of an M. iowae gene encoding a homolog of Mycoplasma pneumoniae CARDS toxin were 5-fold lower in cells grown in low O2. These data suggest that reduced O2, representing the intestinal environment, triggers M. iowae to reduce its virulence capabilities, effecting a change from a pathogenic mode to a potentially beneficial one.
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Affiliation(s)
- Rachel E Pritchard
- Department of Microbiology, Miami University, Oxford, OH, 45056, USA. .,Present address: Division of Natural Sciences and Mathematics, Kentucky Wesleyan College, Owensboro, KY, 42301, USA.
| | - Mitchell F Balish
- Department of Microbiology, Miami University, Oxford, OH, 45056, USA.
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Bravo AL, Sigala JC, Le Borgne S, Morales M. Expression of an alkane monooxygenase (alkB) gene and methyl tert-butyl ether co-metabolic oxidation in Pseudomonas citronellolis. Biotechnol Lett 2014; 37:807-14. [DOI: 10.1007/s10529-014-1737-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 11/20/2014] [Indexed: 11/30/2022]
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Kong W, Li W, Romancova I, Prášil O, Morgan-Kiss RM. An integrated study of photochemical function and expression of a key photochemical gene (psbA) in photosynthetic communities of Lake Bonney (McMurdo Dry Valleys, Antarctica). FEMS Microbiol Ecol 2014; 89:293-302. [DOI: 10.1111/1574-6941.12296] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 01/31/2014] [Accepted: 01/31/2014] [Indexed: 11/27/2022] Open
Affiliation(s)
- Weidong Kong
- Department of Microbiology; Miami University; Oxford OH USA
| | - Wei Li
- Department of Microbiology; Miami University; Oxford OH USA
| | - Ingrid Romancova
- Laboratory of Photosynthesis; Algatech; Institute of Microbiology ASCR; Trebon Czech Republic
| | - Ondřej Prášil
- Laboratory of Photosynthesis; Algatech; Institute of Microbiology ASCR; Trebon Czech Republic
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Estimating the biodegradation of pesticide in soils by monitoring pesticide-degrading gene expression. Biodegradation 2012; 24:203-13. [PMID: 22991035 DOI: 10.1007/s10532-012-9574-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Accepted: 07/09/2012] [Indexed: 10/28/2022]
Abstract
Assessing in situ microbial abilities of soils to degrade pesticides is of great interest giving insight in soil filtering capability, which is a key ecosystem function limiting pollution of groundwater. Quantification of pesticide-degrading gene expression by reverse transcription quantitative PCR (RT-qPCR) was tested as a suitable indicator to monitor pesticide biodegradation performances in soil. RNA extraction protocol was optimized to enhance the yield and quality of RNA recovered from soil samples to perform RT-qPCR assays. As a model, the activity of atrazine-degrading communities was monitored using RT-qPCRs to estimate the level of expression of atzD in five agricultural soils showing different atrazine mineralization abilities. Interestingly, the relative abundance of atzD mRNA copy numbers was positively correlated to the maximum rate and to the maximal amount of atrazine mineralized. Our findings indicate that the quantification of pesticide-degrading gene expression may be suitable to assess biodegradation performance in soil and monitor natural attenuation of pesticide.
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Kong W, Dolhi JM, Chiuchiolo A, Priscu J, Morgan-Kiss RM. Evidence of form II RubisCO (cbbM) in a perennially ice-covered Antarctic lake. FEMS Microbiol Ecol 2012; 82:491-500. [PMID: 22703237 DOI: 10.1111/j.1574-6941.2012.01431.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2012] [Revised: 06/10/2012] [Accepted: 06/11/2012] [Indexed: 11/27/2022] Open
Affiliation(s)
- Weidong Kong
- Department of Microbiology; Miami University; Oxford; OH; USA
| | - Jenna M. Dolhi
- Department of Microbiology; Miami University; Oxford; OH; USA
| | - Amy Chiuchiolo
- Department of Land Resources and Environmental Sciences; Montana State University; Bozeman; MT; USA
| | - John Priscu
- Department of Land Resources and Environmental Sciences; Montana State University; Bozeman; MT; USA
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Diversity and expression of RubisCO genes in a perennially ice-covered Antarctic lake during the polar night transition. Appl Environ Microbiol 2012; 78:4358-66. [PMID: 22492447 DOI: 10.1128/aem.00029-12] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The autotrophic communities in the lakes of the McMurdo Dry Valleys, Antarctica, have generated interest since the early 1960s owing to low light transmission through the permanent ice covers, a strongly bimodal seasonal light cycle, constant cold water temperatures, and geographical isolation. Previous work has shown that autotrophic carbon fixation in these lakes provides an important source of organic matter to this polar desert. Lake Bonney has two lobes separated by a shallow sill and is one of several chemically stratified lakes in the dry valleys that support year-round biological activity. As part of an International Polar Year initiative, we monitored the diversity and abundance of major isoforms of RubisCO in Lake Bonney by using a combined sequencing and quantitative PCR approach during the transition from summer to polar winter. Form ID RubisCO genes related to a stramenopile, a haptophyte, and a cryptophyte were identified, while primers specific for form IA/B RubisCO detected a diverse autotrophic community of chlorophytes, cyanobacteria, and chemoautotrophic proteobacteria. Form ID RubisCO dominated phytoplankton communities in both lobes of the lake and closely matched depth profiles for photosynthesis and chlorophyll. Our results indicate a coupling between light availability, photosynthesis, and rbcL mRNA levels in deep phytoplankton populations. Regulatory control of rbcL in phytoplankton living in nutrient-deprived shallow depths does not appear to be solely light dependent. The distinct water chemistries of the east and west lobes have resulted in depth- and lobe-dependent variability in RubisCO diversity, which plays a role in transcriptional activity of the key gene responsible for carbon fixation.
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Baldwin BR, Biernacki A, Blair J, Purchase MP, Baker JM, Sublette K, Davis G, Ogles D. Monitoring gene expression to evaluate oxygen infusion at a gasoline-contaminated site. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2010; 44:6829-6834. [PMID: 20681521 DOI: 10.1021/es101356t] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Increasingly, molecular biological tools, most notably quantitative polymerase chain reaction (qPCR), are being employed to provide a more comprehensive assessment of bioremediation of petroleum hydrocarbons and fuel oxygenates. While qPCR enumeration of key organisms or catabolic genes can aid in site management decisions, evaluation of site activities conducted to stimulate biodegradation would ideally include a direct measure of gene expression to infer activity. In the current study, reverse-transcriptase (RT) qPCR was used to monitor gene expression to evaluate the effectiveness of an oxygen infusion system to promote biodegradation of BTEX and MTBE. During system operation, dissolved oxygen (DO) levels at the infusion points were greater than 30 mg/L, contaminant concentrations decreased, and transcription of two aromatic oxygenase genes and Methylibium petroleiphilum PM1-like 16S rRNA copies increased by as many as 5 orders of magnitude. Moreover, aromatic oxygenase gene transcription and PM1 16s rRNA increased at downgradient locations despite low DO levels even during system operation. Conversely, target gene expression substantially decreased when the system was deactivated. RT-qPCR results also corresponded to increases in benzene and MTBE attenuation rates. Overall, monitoring gene expression complemented traditional groundwater analyses and conclusively demonstrated that the oxygen infusion system promoted BTEX and MTBE biodegradation.
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Affiliation(s)
- Brett R Baldwin
- Microbial Insights, Inc., Rockford, Tennessee 37853-3044, USA
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