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Xue Y, Jin T, Gao C, Li C, Zhou T, Wan D, Yang M. Effects of biodegradable film mulching on bacterial diversity in soils. Arch Microbiol 2022; 204:195. [PMID: 35217920 DOI: 10.1007/s00203-022-02799-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 02/09/2022] [Accepted: 02/10/2022] [Indexed: 11/30/2022]
Abstract
The spread of biodegradable plastic films (BDFs) not only increases grain yield but also reduces environmental pollution from plastic film to a large extent. Soil microbes are considered to be involved in biodegradation processes. However, the study of microbe diversity in soil mulched with biodegradable plastic film remains limited. Here, we compared the diversity of microbes between soils with biodegradable film and nonbiodegradable film (NBDF) mulch. The results showed that BDFs affected total C, P and NH4+-N, especially organism C content, as well as microbe species richness (ACE; Chao1) and diversity (Simpson index; Shannon index). In terms of dominant phyla and genera, BDFs and NBDF can influence the abundance of disparate species. Furthermore, BDFs could also contribute to improving the richness of the important functional bacterial groups in soil, e.g., Pedomicrobium and Comamonas, both of which are involved in the degradation of plastic residues in soil. Finally, we found that BDFs improved the transformation of nitrogen by significantly increasing the abundances of Nitrobacter and Nitrospira. Our results highlight the impact of BDF mulch on the abundance of functional bacteria in the soil.
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Affiliation(s)
- Yinghao Xue
- College of Land and Environment, Shenyang Agricultural University, Shenyang, 110866, China.,Rural Energy and Environment Agency, Ministry of Agriculture and Rural Affairs, Beijing, 100125, China
| | - Tuo Jin
- Rural Energy and Environment Agency, Ministry of Agriculture and Rural Affairs, Beijing, 100125, China
| | - Chengyu Gao
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, Gansu, People's Republic of China
| | - Chongxiao Li
- Agricultural Ecology and Resource Protection Technology Extension Station of Gansu Province, Lanzhou, 730000, Gansu, People's Republic of China
| | - Tao Zhou
- Agricultural Ecology and Resource Protection Technology Extension Station of Gansu Province, Lanzhou, 730000, Gansu, People's Republic of China
| | - Dongshi Wan
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, Gansu, People's Republic of China.
| | - Mengran Yang
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, Gansu, People's Republic of China.
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Chen H, Zhang C, Rao Y, Jing Y, Luo G, Zhang S. Methane potentials of wastewater generated from hydrothermal liquefaction of rice straw: focusing on the wastewater characteristics and microbial community compositions. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:140. [PMID: 28580014 PMCID: PMC5452606 DOI: 10.1186/s13068-017-0830-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 05/26/2017] [Indexed: 05/13/2023]
Abstract
BACKGROUND Hydrothermal liquefaction (HTL) has been well studied for the bio-oil production from biomass. However, a large amount of wastewater with high organic content is also produced during the HTL process. Therefore, the present study investigated the methane potentials of hydrothermal liquefaction wastewater (HTLWW) obtained from HTL of rice straw at different temperatures (170-320 °C) and residence times (0.5-4 h). The characteristics (e.g., total organic content, organic species, molecular size distribution, etc.) of the HTLWW were studied, and at the same time, microbial community compositions involved in AD of HTLWW were analyzed. RESULTS The highest methane yield of 314 mL CH4/g COD was obtained from the sample 200 °C-0.5 h (HTL temperature at 200 °C for 0.5 h), while the lowest methane yield 217 mL CH4/g COD was obtained from the sample 320 °C-0.5 h. These results were consistent with the higher amounts of hard biodegradable organics (furans, phenols, etc.) and lower amounts of easily biodegradable organics (sugars and volatile fatty acids) present in sample 320 °C-0.5 h compared to sample 200 °C-0.5 h. Size distribution analysis showed that sample 320 °C-0.5 h contained more organics with molecular size less than 1 kDa (79.5%) compared to sample 200 °C-0.5 h (66.2%). Further studies showed that hard biodegradable organics were present in the organics with molecular size higher than 1 kDa for sample 200 °C-0.5 h. In contrast, those organics were present in both the organics with molecular size higher and less than 1 kDa for sample 320 °C-0.5 h. Microbial community analysis showed that different microbial community compositions were established during the AD with different HTLWW samples due to the different organic compositions. For instance, Petrimonas, which could degrade sugars, had higher abundance in the AD of sample 200 °C-0.5 h (20%) compared to sample 320 °C-0.5 h (7%). The higher abundance of Petrimonas was consistent with the higher content of sugars in sample 200 °C-0.5 h. The higher Petrimonas abundance was consistent with the higher content of sugars in sample 200 °C-0.5 h. The genus Syntrophorhabdus could degrade phenols and its enrichment in the AD of sample 320 °C-0.5 h might be related with the highest content of phenols in the HTLWW. CONCLUSIONS HTL parameters like temperature and residence time affected the biodegradability of HTLWW obtained from HTL of rice straw. More hard biodegradable organics were produced with the increase of HTL temperature. The microbial community compositions during the AD were also affected by the different organic compositions in HTLWW samples.
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Affiliation(s)
- Huihui Chen
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai, 200433 China
| | - Cheng Zhang
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai, 200433 China
| | - Yue Rao
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai, 200433 China
| | - Yuhang Jing
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai, 200433 China
| | - Gang Luo
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai, 200433 China
| | - Shicheng Zhang
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai, 200433 China
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hypD as a marker for [NiFe]-hydrogenases in microbial communities of surface waters. Appl Environ Microbiol 2014; 80:3776-82. [PMID: 24727276 DOI: 10.1128/aem.00690-14] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Hydrogen is an important trace gas in the atmosphere. Soil microorganisms are known to be an important part of the biogeochemical H2 cycle, contributing 80 to 90% of the annual hydrogen uptake. Different aquatic ecosystems act as either sources or sinks of hydrogen, but the contribution of their microbial communities is unknown. [NiFe]-hydrogenases are the best candidates for hydrogen turnover in these environments since they are able to cope with oxygen. As they lack sufficiently conserved sequence motifs, reliable markers for these enzymes are missing, and consequently, little is known about their environmental distribution. We analyzed the essential maturation genes of [NiFe]-hydrogenases, including their frequency of horizontal gene transfer, and found hypD to be an applicable marker for the detection of the different known hydrogenase groups. Investigation of two freshwater lakes showed that [NiFe]-hydrogenases occur in many prokaryotic orders. We found that the respective hypD genes cooccur with oxygen-tolerant [NiFe]-hydrogenases (groups 1 and 5) mainly of Actinobacteria, Acidobacteria, and Burkholderiales; cyanobacterial uptake hydrogenases (group 2a) of cyanobacteria; H2-sensing hydrogenases (group 2b) of Burkholderiales, Rhizobiales, and Rhodobacterales; and two groups of multimeric soluble hydrogenases (groups 3b and 3d) of Legionellales and cyanobacteria. These findings support and expand a previous analysis of metagenomic data (M. Barz et al., PLoS One 5:e13846, 2010, http://dx.doi.org/10.1371/journal.pone.0013846) and further identify [NiFe]-hydrogenases that could be involved in hydrogen cycling in aquatic surface waters.
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Roumagnac P, Richaud P, Barakat M, Ortet P, Roncato MA, Heulin T, Peltier G, Achouak W, Cournac L. Reversible oxygen-tolerant hydrogenase carried by free-living N2-fixing bacteria isolated from the rhizospheres of rice, maize, and wheat. Microbiologyopen 2012; 1:349-61. [PMID: 23233392 PMCID: PMC3535381 DOI: 10.1002/mbo3.37] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Revised: 08/07/2012] [Accepted: 08/08/2012] [Indexed: 12/03/2022] Open
Abstract
Hydrogen production by microorganisms is often described as a promising sustainable and clean energy source, but still faces several obstacles, which prevent practical application. Among them, oxygen sensitivity of hydrogenases represents one of the major limitations hampering the biotechnological implementation of photobiological production processes. Here, we describe a hierarchical biodiversity-based approach, including a chemochromic screening of hydrogenase activity of hundreds of bacterial strains collected from several ecosystems, followed by mass spectrometry measurements of hydrogenase activity of a selection of the H2-oxidizing bacterial strains identified during the screen. In all, 131 of 1266 strains, isolated from cereal rhizospheres and basins containing irradiating waste, were scored as H2-oxidizing bacteria, including Pseudomonas sp., Serratia sp., Stenotrophomonas sp., Enterobacter sp., Rahnella sp., Burkholderia sp., and Ralstonia sp. isolates. Four free-living N2-fixing bacteria harbored a high and oxygen-tolerant hydrogenase activity, which was not fully inhibited within entire cells up to 150–250 μmol/L O2 concentration or within soluble protein extracts up to 25–30 μmol/L. The only hydrogenase-related genes that we could reveal in these strains were of the hyc type (subunits of formate hydrogenlyase complex). The four free-living N2-fixing bacteria were closely related to Enterobacter radicincitans based on the sequences of four genes (16S rRNA, rpoB, hsp60, and hycE genes). These results should bring interesting prospects for microbial biohydrogen production and might have ecophysiological significance for bacterial adaptation to the oxic–anoxic interfaces in the rhizosphere.
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Affiliation(s)
- Philippe Roumagnac
- CIRAD, UMR BGPI, Campus International de Montferrier-Baillarguet, F-34398, Montpellier Cedex-5, France
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Cultivation-independent detection of autotrophic hydrogen-oxidizing bacteria by DNA stable-isotope probing. Appl Environ Microbiol 2011; 77:4931-8. [PMID: 21622787 DOI: 10.1128/aem.00285-11] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Knallgas bacteria are a physiologically defined group that is primarily studied using cultivation-dependent techniques. Given that current cultivation techniques fail to grow most bacteria, cultivation-independent techniques that selectively detect and identify knallgas bacteria will improve our ability to study their diversity and distribution. We used stable-isotope probing (SIP) to identify knallgas bacteria in rhizosphere soil of legumes and in a microbial mat from Obsidian Pool in Yellowstone National Park. When samples were incubated in the dark, incorporation of (13)CO(2) was H(2) dependent. SIP enabled the detection of knallgas bacteria that were not detected by cultivation, and the majority of bacteria identified in the rhizosphere soils were betaproteobacteria predominantly related to genera previously known to oxidize hydrogen. Bacteria in soil grew on hydrogen at concentrations as low as 100 ppm. A hydB homolog encoding a putative high-affinity NiFe hydrogenase was amplified from (13)C-labeled DNA from both vetch and clover rhizosphere soil. The results indicate that knallgas bacteria can be detected by SIP and populations that respond to different H(2) concentrations can be distinguished. The methods described here should be applicable to a variety of ecosystems and will enable the discovery of additional knallgas bacteria that are resistant to cultivation.
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Barz M, Beimgraben C, Staller T, Germer F, Opitz F, Marquardt C, Schwarz C, Gutekunst K, Vanselow KH, Schmitz R, LaRoche J, Schulz R, Appel J. Distribution analysis of hydrogenases in surface waters of marine and freshwater environments. PLoS One 2010; 5:e13846. [PMID: 21079771 PMCID: PMC2974642 DOI: 10.1371/journal.pone.0013846] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2010] [Accepted: 09/17/2010] [Indexed: 12/31/2022] Open
Abstract
Background Surface waters of aquatic environments have been shown to both evolve and consume hydrogen and the ocean is estimated to be the principal natural source. In some marine habitats, H2 evolution and uptake are clearly due to biological activity, while contributions of abiotic sources must be considered in others. Until now the only known biological process involved in H2 metabolism in marine environments is nitrogen fixation. Principal Findings We analyzed marine and freshwater environments for the presence and distribution of genes of all known hydrogenases, the enzymes involved in biological hydrogen turnover. The total genomes and the available marine metagenome datasets were searched for hydrogenase sequences. Furthermore, we isolated DNA from samples from the North Atlantic, Mediterranean Sea, North Sea, Baltic Sea, and two fresh water lakes and amplified and sequenced part of the gene encoding the bidirectional NAD(P)-linked hydrogenase. In 21% of all marine heterotrophic bacterial genomes from surface waters, one or several hydrogenase genes were found, with the membrane-bound H2 uptake hydrogenase being the most widespread. A clear bias of hydrogenases to environments with terrestrial influence was found. This is exemplified by the cyanobacterial bidirectional NAD(P)-linked hydrogenase that was found in freshwater and coastal areas but not in the open ocean. Significance This study shows that hydrogenases are surprisingly abundant in marine environments. Due to its ecological distribution the primary function of the bidirectional NAD(P)-linked hydrogenase seems to be fermentative hydrogen evolution. Moreover, our data suggests that marine surface waters could be an interesting source of oxygen-resistant uptake hydrogenases. The respective genes occur in coastal as well as open ocean habitats and we presume that they are used as additional energy scavenging devices in otherwise nutrient limited environments. The membrane-bound H2-evolving hydrogenases might be useful as marker for bacteria living inside of marine snow particles.
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Affiliation(s)
- Martin Barz
- Botanisches Institut, Christian-Albrechts-Universität, Kiel, Germany
| | | | - Torsten Staller
- Forschungs- und Technologiezentrum Westküste (FTZ) der Christian-Albrechts-Universität, Büsum, Germany
| | - Frauke Germer
- Botanisches Institut, Christian-Albrechts-Universität, Kiel, Germany
| | - Friederike Opitz
- Botanisches Institut, Christian-Albrechts-Universität, Kiel, Germany
| | - Claudia Marquardt
- Botanisches Institut, Christian-Albrechts-Universität, Kiel, Germany
| | - Christoph Schwarz
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - Kirstin Gutekunst
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - Klaus Heinrich Vanselow
- Forschungs- und Technologiezentrum Westküste (FTZ) der Christian-Albrechts-Universität, Büsum, Germany
| | - Ruth Schmitz
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität, Kiel, Germany
| | - Julie LaRoche
- Leibniz-Institute of Marine Sciences, IFM-GEOMAR, Kiel, Germany
| | - Rüdiger Schulz
- Botanisches Institut, Christian-Albrechts-Universität, Kiel, Germany
| | - Jens Appel
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
- * E-mail:
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Maimaiti J, Zhang Y, Yang J, Cen YP, Layzell DB, Peoples M, Dong Z. Isolation and characterization of hydrogen-oxidizing bacteria induced following exposure of soil to hydrogen gas and their impact on plant growth. Environ Microbiol 2007; 9:435-44. [PMID: 17222141 DOI: 10.1111/j.1462-2920.2006.01155.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In many legumes, the nitrogen fixing root nodules produce H2 gas that diffuses into soil. It has been demonstrated that such exposure of soil to H2 can promote plant growth. To assess whether this may be due to H2-oxidizing microorganisms, bacteria were isolated from soil treated with H2 under laboratory conditions and from soils collected adjacent to H2 producing soybean nodules. Nineteen isolates of H2-oxidizing bacteria were obtained and all exhibited a half-saturation coefficient (Ks) for H2 of about 1 ml l(-1). The isolates were identified as Variovorax paradoxus, Flavobacterium johnsoniae and Burkholderia spp. using conventional microbiological tests and 16S rRNA gene sequence analysis. Seventeen of the isolates enhanced (57-254%) root elongation of spring wheat seedlings. Using an Arabidopsis thaliana bioassay, plant biomass was increased by 11-27% when inoculated by one of four isolates of V. paradoxus or one isolate of Burkholderia that were selected for evaluation. The isolates of V. paradoxus found in both H2-treated soil and in soil adjacent to soybean nodules had the greatest impact on plant growth. The results are consistent with the hypothesis that H2-oxidizing bacteria in soils have plant growth promoting properties.
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Affiliation(s)
- Jiamila Maimaiti
- Department of Biology, St. Mary's University, Halifax, NS, Canada, B3H 3C3
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Bjerrum L, Kjaer T, Ramsing NB. Enumerating ammonia-oxidizing bacteria in environmental samples using competitive PCR. J Microbiol Methods 2002; 51:227-39. [PMID: 12133615 DOI: 10.1016/s0167-7012(02)00077-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Primers targeting part of the ammonia-monooxygenase gene (amoA) have been used to detect and characterize ammonia-oxidizing bacteria (AOB) in different environments. In this study, a quantitative polymerase chain reaction (PCR) technique using a competitive template for the amoA primer pair is described and evaluated. The method is based on addition of an internal standard to the PCR, a competitive template, which is amplified together with the template in the environmental sample. By adding different amounts of competitive template to the sample and observing the relative intensity of environmental amplificate and competitive amplificate, the number of amoA gene copies can be determined. Different tests were made to evaluate the competitive PCR method (cPCR) with respect to equal amplification efficiency of the two templates, degeneracy of the priming site and the importance of flanking regions surrounding the competitive template. Calibration curves made by addition of known amounts of Nitrosomonas europaea to soil samples revealed a detection limit for this technique of less than 1000 cells g(-1) soil and a linear response over a wide range of cell additions. Cloning and sequencing of amoA amplificates have confirmed the specificity of the primers, as we have not detected any false positives among the more than 200 clones investigated. The vertical distribution of ammonia-oxidizers in the upper cm of a waterlogged rice paddy soil was compared to nitrate and oxygen concentration profiles determined with microsensors and to net process rates derived from these profiles.
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Affiliation(s)
- Lotte Bjerrum
- Department of Microbial Ecology, Institute of Biological Sciences, University of Aarhus, Ny Munkegade, Building 540, DK-8000, Aarhus, Denmark
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Michotey V, Méjean V, Bonin P. Comparison of methods for quantification of cytochrome cd(1)-denitrifying bacteria in environmental marine samples. Appl Environ Microbiol 2000; 66:1564-71. [PMID: 10742243 PMCID: PMC92024 DOI: 10.1128/aem.66.4.1564-1571.2000] [Citation(s) in RCA: 155] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Two PCR primer sets were developed for the detection and quantification of cytochrome cd(1)-denitrifying bacteria in environmental marine samples. The specificity and sensitivity of these primers were tested. Both primer sets were suitable for detection, but only one set, cd3F-cd4R, was suitable for the quantification and enumeration of the functional community using most-probable-number PCR and competitive PCR techniques. Quantification of cytochrome cd(1) denitrifiers taken from marine sediment and water samples was achieved using two different molecular techniques which target the nirS gene, and the results were compared to those obtained by using the classical cultivation method. Enumerations using both molecular techniques yielded similar results in seawater and sediment samples. However, both molecular techniques showed 1,000 or 10 times more cytochrome cd(1) denitrifiers in the sediment or water samples, respectively, than were found by use of the conventional cultivation method for counting.
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Affiliation(s)
- V Michotey
- Laboratoire d'Océanologie et de Biogeochimie, CNRS-UMR 6535, Centre d'Océanologie de Marseille, Campus de Luminy, 13288 Marseille cedex 9, France.
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Johnsen K, Enger O, Jacobsen CS, Thirup L, Torsvik V. Quantitative selective PCR of 16S ribosomal DNA correlates well with selective agar plating in describing population dynamics of indigenous Pseudomonas spp. in soil hot spots. Appl Environ Microbiol 1999; 65:1786-8. [PMID: 10103283 PMCID: PMC91253 DOI: 10.1128/aem.65.4.1786-1788.1999] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We used a quantitative PCR method targeting 16S ribosomal DNA using competitive PCR for specific detection of indigenous Pseudomonas DNA in soil hot spots. The amount of Pseudomonas DNA corresponded to the number of culturable Pseudomonas bacteria on Gould's S1 agar. This represents the first use of PCR for quantification of indigenous bacteria in more than one sample of soil.
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Affiliation(s)
- K Johnsen
- Geological Survey of Denmark and Greenland, Copenhagen, Denmark.
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