Diazotrophic Community Structure Research Articles

Response of symbiotic and asymbiotic nitrogen-fixing microorganisms to nitrogen fertilizer application

Biological nitrogen fixation (BNF) plays an important role in nitrogen cycling by transferring atmospheric dinitrogen to the soil. BNF is performed by symbiotic and asymbiotic nitrogen-fixing microorganisms. However, the abundance, activity, and community structure of diazotrophs under different nitrogen fertilizer application rates and how root exudates influence diazotrophs remain unclear. 15N-N2 and 13C-CO2 labeling, DNA-based stable isotope probing (SIP), and molecular biological techniques were used in this study. The abundance, activity, and structure of symbiotic and asymbiotic diazotrophs under different nitrogen fertilizer applications in paddy soil were investigated. We found that the nitrogen fixation capacity in milk vetch (Astragalus sinicus L.) and nifH gene abundance in the root nodules were significantly higher in the low-nitrogen treatment than in the control (zero) and high-nitrogen treatments. Nitrogen-fixing bacteria were abundant in the soils with a high biodiversity. Soil nifH gene sequences were dominated by α-, β-, and δ-proteobacteria, as well as by Cyanobacteria. The relative abundance of α-proteobacteria was lower, and the relative abundance of Cyanobacteria was higher under high nitrogen. Incubation of soil with 13CO2 and subsequent DNA-SIP analysis demonstrated that OTU65 from α-proteobacteria was relatively more abundant in heavy fractions of the 13C-labeled soils than that in the unlabeled soils, indicating that α-proteobacteria may prefer rhizodeposition carbon to other organic carbon. However, OTU24 and OTU73 from δ-proteobacteria had relatively high abundances in light fractions both in the 13C-labeled and unlabeled samples, indicating that δ-proteobacteria may prefer other soil organic carbon to rhizodeposition carbon. The results suggested that soil N availability and rhizodeposition strongly modified the microbial communities of nitrogen-fixing bacteria. Moderate nitrogen application increased the symbiotic biological N fixing activity in the Astragalus sinicus L. rhizosphere. The BNF activity in the legume-rhizobia system is regulated by the exchange of organic C and N nutrient between the host plant and N-fixing bacteria.

Long-term fertilization influences community assembly processes of soil diazotrophs

Unraveling the drivers of microbial community variation in response to different environmental conditions is a major goal in ecology. Although diazotrophs play a dominant role in global biological nitrogen (N2) fixation, the controls on soil diazotrophic community assembly are not fully understood. In this study, we investigated soil diazotrophic communities in field plots that received long-term (30 years) fertilization treatments with Illumina MiSeq sequencing. Long-term chemical fertilization significantly changed soil diazotrophic community structure and resulted in the decrease of diazotrophic diversity, while the addition of livestock manure could maintain the diversity. Diazotrophic community structure and diversity were mostly correlated with soil pH. Deterministic processes structured diazotrophic communities in both unfertilized and fertilized soils. However, the deterministic selection on phylogenetically non-conserved traits increased phylogenetic randomness in all fertilized treatments. These trends for diazotrophs differed from those for the entire bacterial community, which was structured through deterministic processes and exhibited phylogenetic nonrandomness in unfertilized and fertilized soils. Taken together, our results indicated that long-term fertilization strongly affected the diversity, community structure and assembly processes of soil diazotrophs, which may have implications for the rate of biological N2 fixation in agricultural systems.

Linkage Between Dinitrogen Fixation and Primary Production in the Oligotrophic South Pacific Ocean

AbstractThe import of nitrogen via dinitrogen fixation supports primary production, particularly in the oligotrophic ocean; however, to what extent dinitrogen fixation influences primary production, and the role of specific types of diazotrophs, remains poorly understood. We examined the relationship between primary production and dinitrogen fixation together with diazotroph community structure in the oligotrophic western and eastern South Pacific Ocean and found that dinitrogen fixation was higher than nitrate‐based new production. Primary production increased in the middle of the western subtropical region, where the cyanobacterium Trichodesmium dominated the diazotroph community and accounted for up to 7.8% of the phytoplankton community, and the abundance of other phytoplankton taxa (especially Prochlorococcus) was high. These results suggest that regenerated production was enhanced by nitrogen released from Trichodesmium and that carbon fixation by Trichodesmium also contributed significantly to total primary production. Although volumetric dinitrogen fixation was comparable between the western and eastern subtropical regions, primary production in the western waters was more than twice as high as that in the eastern waters, where UCYN‐A1 (photoheterotroph) and heterotrophic bacteria were the dominant diazotrophs. This suggests that dinitrogen fixed by these diazotrophs contributed relatively little to primary production of the wider community, and there was limited carbon fixation by these diazotrophs. Hence, we document how the community composition of diazotrophs in the field can be reflected in how much nitrogen becomes available to the wider phytoplankton community and in how much autotrophic diazotrophs themselves fix carbon and thereby influences the magnitude of local primary production.

Diazotroph community structure and the role of nitrogen fixation in the nitrogen cycle in the Chukchi Sea (western Arctic Ocean)

AbstractMarine nitrogen fixation occurs not only in subtropical and tropical regions but also in colder regions. However, the distribution of diazotrophs, nitrogen fixation rate, and its contribution to the nitrogen cycle in the Arctic Ocean remain poorly understood. We examined the diazotroph community structure and activity in the shelf and off‐shelf regions of the Chukchi Sea, western Arctic Ocean, during late summer 2015. The nitrate and ammonium assimilation rates were determined simultaneously to gain insights into the role of nitrogen fixation in the nitrogen cycle of the region. The diazotroph community determined by Illumina sequencing was mainly composed of Cluster III nifH phylotypes (putative anaerobes), accounting for > 80% of the total sequences examined, except for one surface sample. This result is strikingly different from previous findings in other oceanic regions. The nifH sequences other than those from Cluster III were mostly affiliated with UCYN‐A2 (symbiotic cyanobacteria), which accounted for < 15% of the total sequences. UCYN‐A2 tended to be abundant (maximum 2.9 × 103 copies L−1) in the high‐temperature low‐salinity water mass that is characteristic of Pacific‐originating water. Nitrogen fixation rate was detectable at most stations, with a range of 0.08–3.60 nmol L−1 d−1, displaying no clear relationship with depth (light intensity) or nitrate or ammonium concentration. Nitrogen fixation locally exceeded nitrate assimilation, but accounted for 1.00% at most in the total nitrogen assimilation in the euphotic zone.

Long-term application of lime or pig manure rather than plant residues suppressed diazotroph abundance and diversity and altered community structure in an acidic Ultisol

Biological fixation of atmospheric dinitrogen (N2) is an important process that replenishes biologically available nitrogen (N) in soil and helps minimize the use of inorganic N fertilizer in agricultural ecosystems. Diazotrophs are key fixers of atmospheric N2 in a range of soil types, however, there is uncertainty about how they respond to long-term fertilization. Here, using the nifH gene as a molecular marker, we investigated the long-term effects of inorganic and organic fertilization on diazotroph abundance and community structure in an acidic Ultisol. The field experiment ran for 27 years and comprised seven treatments: no fertilization (control); inorganic NPK fertilizer (N); inorganic NPK fertilizer + lime (CaCO3) (NL); inorganic NPK fertilizer + peanut straw (NPS); inorganic NPK fertilizer + rice straw (NRS); inorganic NPK fertilizer + radish (NR); and inorganic NPK fertilizer + pig manure (NPM). Long-term application of fertilizer reduced the abundance and diversity of nifH gene compared with the control (P < 0.05), while lime and pig manure increased the inhibitory effects (P < 0.05). The abundance and diversity of nifH genes were negatively correlated with soil pH, indicating that increasing soil pH potentially affect N fixation ability in acidic Ultisols. Community structure of diazotrophs in the NPS, NRS, and NR treatments were similar and shared most operational taxonomic units (OTUs) with the N treatment, with only a minor difference to that of the control. Thus, there was no effect of plant residue types on diazotroph community structure. In contrast, the application of inorganic fertilizer + liming or pig manure altered the diazotroph community structure with shifts in the dominant genus, from Bradyrhizobium in the control to Azohydromonas in NL and Azospirillum in NPM. Soil pH was the key factor correlated with change in diazotroph community structure. Overall, our results suggested that regular use of lime or pig manure rather than different types of plant residue reduced the abundance and diversity and altered community structure of diazotrophs, that may potentially affect N fixation ability in acidic Ultisols.

Soil pH correlates with the co-occurrence and assemblage process of diazotrophic communities in rhizosphere and bulk soils of wheat fields

Biological nitrogen fixation contributes to the pool of plant-available N in both bulk soil and the rhizosphere. Here we investigated the co-association and assemblage process of diazotrophic community members in both rhizosphere and bulk soil of wheat fields. The diazotrophic community structure in the rhizosphere was significantly different and comprised a less competitive and more stable network structure when compared with that of the bulk soil. Deterministic versus stochastic community assemblage processes were quantified using betaNTI scores, demonstrating that deterministic processes decreased in importance with distance from plant roots. Soil pH was correlated with diazotrophic community structure and diversity, and community structure showed greater connectivity and stability in soils with neutral pH relative to those in acidic or alkaline soils. Stochastic processes dominated the assemblage of the diazotrophic community in soils with neutral pH, while deterministic processes dominated in acidic or alkaline soils. These results suggest that soil pH may play an essential role in the interaction and assemblage processes of the diazotrophic community in the rhizosphere and bulk soils, which could enhance our understanding of biological nitrogen fixation in agricultural soils.

Long-term manure addition reduces diversity and changes community structure of diazotrophs in a neutral black soil of northeast China

Although biological nitrogen fixation is an important nitrogen source for agroecosystem, the knowledge of their response to long-term fertilization under neutral soil is limited. The aims of this study were to explore the effects of different fertilization treatments on diversity and compositions of diazotrophic community in a neutral black soil in northeast China. The long-term fertilization experiment under monoculture maize was established in a neutral black soil since 1979. Soil samples from four treatments were collected in September 2014: non-fertilization (NoF), chemical fertilization (CF), manure fertilization (M), and chemical fertilization plus manure (CFM). qPCR and Illumina MiSeq sequencing were used to assess the abundance and compositions of diazotrophic community targeting nifH gene. M treatment significantly increased the nifH gene abundance, but inverse trends were found in the CF and CFM treatments when compared with NoF. The diazotrophic community was overwhelmingly dominated by Alphaproteobacteria with relative higher abundance in manure-added treatments. Principal coordinate analysis (PCoA) indicated that the total diazotrophic community was separated into two groups with and without manure addition, and soil available P was the most influential factor on the changes of diazotrophic community. Our results suggested that soil nutrients rather than soil pH were the main influential factors on the changes of diazotrophic communities and manure addition had a greater effect than chemical fertilization on diazotrophic community structure in neutral black soil.

Influence of nitrogen and phosphorus additions on N2-fixation activity, abundance, and composition of diazotrophic communities in a Chinese fir plantation

Although biological nitrogen (N) fixation (BNF) is an important N input process in subtropical forest ecosystems, how the diazotrophic communities related to this process respond to N and phosphorus (P) inputs is largely unknown. We investigated the effects of exogenous N and/or P inputs on N2-fixation activity, diazotrophic abundance and community composition using a continuous application of fertilizers over 5years experiment in a Chinese fir plantation. The fertilization regimes included control (CK), P treatment (P), low N addition treatment (N1), high N addition treatment (N2), low N and P addition treatment (N1P) and high N with P addition treatment (N2P). N2-fixation activity was determined using the acetylene reduction assay (ARA). Quantitative PCR and Illumina Miseq sequencing of nifH gene were performed to analyze diazotrophic abundance and community composition, respectively. Our results showed that P addition increased N2-fixation activity and nifH gene abundance by 189.07nmol C2H4 and 1.02×107copiesg−1 dry soil, respectively, while were reduced by 1.19nmol C2H4 and 2.04×106copiesg−1 dry soil when N was added. The application of P with low N (N1P) effectively alleviated the inhibitory effect of N input on N2-fixation activity. N-related treatments resulted in significant decreases in operational taxonomic unit (OTU) richness and shifts in diazotrophic community structure. N2-fixation activity and nifH gene abundance were strongly and positively correlated with soil pH and negatively correlated with mineral N (NH4+-N and NO3−-N) contents, while mineral N concentrations rather than soil pH appeared to be the main factor altering diazotrophic community structure. These results revealed that P addition played a positive role in regulating biological nitrogen fixation in subtropical forest ecosystems.

Diversity and Structure of Diazotrophic Communities in Mangrove Rhizosphere, Revealed by High-Throughput Sequencing.

Diazotrophic communities make an essential contribution to the productivity through providing new nitrogen. However, knowledge of the roles that both mangrove tree species and geochemical parameters play in shaping mangove rhizosphere diazotrophic communities is still elusive. Here, a comprehensive examination of the diversity and structure of microbial communities in the rhizospheres of three mangrove species, Rhizophora apiculata, Avicennia marina, and Ceriops tagal, was undertaken using high-throughput sequencing of the 16S rRNA and nifH genes. Our results revealed a great diversity of both the total microbial composition and the diazotrophic composition specifically in the mangrove rhizosphere. Deltaproteobacteria and Gammaproteobacteria were both ubiquitous and dominant, comprising an average of 45.87 and 86.66% of total microbial and diazotrophic communities, respectively. Sulfate-reducing bacteria belonging to the Desulfobacteraceae and Desulfovibrionaceae were the dominant diazotrophs. Community statistical analyses suggested that both mangrove tree species and additional environmental variables played important roles in shaping total microbial and potential diazotroph communities in mangrove rhizospheres. In contrast to the total microbial community investigated by analysis of 16S rRNA gene sequences, most of the dominant diazotrophic groups identified by nifH gene sequences were significantly different among mangrove species. The dominant diazotrophs of the family Desulfobacteraceae were positively correlated with total phosphorus, but negatively correlated with the nitrogen to phosphorus ratio. The Pseudomonadaceae were positively correlated with the concentration of available potassium, suggesting that diazotrophs potentially play an important role in biogeochemical cycles, such as those of nitrogen, phosphorus, sulfur, and potassium, in the mangrove ecosystem.

Soil pH is a major driver of soil diazotrophic community assembly in Qinghai-Tibet alpine meadows

The biological nitrogen input is essential for nutrient enrichment in natural grassland ecosystems. This process is carried out by diazotrophic microbes. However, the patterns and assembly processes of diazotrophic communities in grassland soil are not fully understood, especially in alpine meadows of high-altitude Qinghai-Tibet Plateau (QTP). In this study, the diversity patterns and community assembly processes of soil diazotrophic communities were investigated in QTP alpine meadows. The results showed that different diazotrophic taxa responded differentially to the increase of soil pH, and α-diversity increased linearly with pH values. Diazotrophic community turnover was enhanced by the increased variation in soil pH, moreover, it also showed strong response to mean annual temperature. Null model analysis showed that deterministic processes were most important in shaping the phylogenetic community structure and assembly of diazotrophs. Diazotrophic communities of each sampling site tended to be phylogenetically clustered, while communities at high pH soils (pH 7.00 to 8.00) showed more clustering than those of low pH (pH 5.02 to 7.00). The soil pH is a main driver in structuring soil diazotrophic community assembly by regulating the relative importance of deterministic and stochastic processes in QTP alpine meadows.

Analysis of nifH-RNA reveals phylotypes related to Geobacter and Cyanobacteria as important functional components of theN2 -fixing community depending on depth and agriculturaluse of soil.

In this survey, a total of 80 787 reads and 28 171 unique NifH protein sequences were retrieved from soil RNA. This dataset extends our knowledge about the structure and diversity of the functional diazotrophic communities in agricultural soils from Argentinean Pampas. Operational taxonomic unit (OTU)‐based analyses showed that nifH phylotypes related to Geobacter and Anaeromyxobacter (44.8%), Rhizobiales (29%), Cyanobacteria (16.7%), and Verrucomicrobiales (8%) are key microbial components of N2 fixation in soils associated with no‐till management and soil depth. In addition, quantification of nifH gene copies related to Geobacter and Cyanobacteria revealed that these groups are abundant in soils under maize–soybean rotation and soybean monoculture, respectively. The correlation of physicochemical soil parameters with the diazotrophic diversity and composition showed that soil stability and organic carbon might contribute to the functional signatures of particular nifH phylotypes in fields under no‐till management. Because crop production relies on soil‐borne microorganism's activities, such as free N2 fixation, the information provided by our study on the diazotrophic population dynamics, associated with the edaphic properties and land‐use practices, represents a major contribution to gain insight into soil biology, in which functionally active components are identified.

Impact of 25 years of inorganic fertilization on diazotrophic abundance and community structure in an acidic soil in southern China

Although diazotrophs are important in the nitrogen (N)-cycle and contribute to the pool of plant available N, the population response to long-term inorganic fertilization is largely unknown. Here, we investigated the diazotrophic populations in both the bulk and rhizosphere soils of maize grown in an acidic farmland soil that experienced 25 years of inorganic fertilization. The fertilization regimes included unfertilized control, N fertilizer alone, N fertilizer with quicklime, phosphorus (P) and potassium (K) fertilizers, N + P + K fertilizers, and N + P + K fertilizers with quicklime. Quantitative PCR and high-throughput pyrosequencing of the nifH gene were used to analyze diazotrophic abundance and community composition. All of the fertilizer treatments improved soil nutrient availability, but those without quicklime caused soil acidification. Maize biomasses and nifH copy numbers were significantly lower under N and N + P + K treatments but increased under P + K fertilization. Quicklime applications effectively alleviated the inhibitory effect of N input. Fertilization led to decreases in operational taxonomic unit richness and shifts in diazotrophic community composition. Soil pH and nutrient availability had a cooperative effect on diazotrophic abundance, while soil nutrient availability appeared to be the main factor shaping diazotrophic community structure. Rhizosphere effects increased the nifH gene copy number but did not obviously change the diazotrophic community composition on the current research scale. Overall, the long-term inorganic fertilization affected both diazotrophic abundance and community composition, and the fertilizer treatment had a greater influence than quicklime remediation or crop cultivation on community composition.

Basin scale variability of active diazotrophs and nitrogen fixation in the North Pacific, from the tropics to the subarctic Bering Sea

AbstractNitrogen‐fixing microorganisms (diazotrophs) provide biologically available nitrogen to plankton communities and thereby greatly influence the productivity in many marine regions. Various cyanobacterial groups have traditionally been considered the major oceanic diazotrophs, but later noncyanobacterial and presumably heterotrophic diazotrophs were also found to be widespread and potentially important in nitrogen fixation. However, the distribution and activity of different diazotroph groups is still poorly constrained for most oceanic ecosystems. Here we examined diazotroph community structure and activity along a 7500 km south‐north transect between the central equatorial Pacific and the Bering Sea. Nitrogen fixation contributed up to 84% of new production in the upper waters of the subtropical gyre, where the diazotroph community included the gammaproteobacterium γ‐24774A11 and highly active cyanobacterial phylotypes (&gt;50% of total nifH transcript abundance). Nitrogen fixation was sometimes detectable down to 150 m depth and extended horizontally to the edge of the gyre at around 35°N. Nitrogen fixation was even detected far north on the Bering Sea shelf. In the Alaskan Coastal Waters on the Bering Sea shelf, low nitrate together with high dissolved iron concentrations seemed to foster diazotroph growth, including a prominent role of UCYN‐A2, which was abundant near the surface (1.2×105 nifH gene copies L−1). Our study provides evidence for nitrogen fixation in the Bering Sea and suggests a clear contrast in the composition of diazotrophs between the tropical/subtropical gyre and the separate waters in the cold northern regions of the North Pacific.

Diversity and activity of nitrogen‐fixing communities across ocean basins

AbstractRecent observations of N2 fixation rates (NFR) and the presence of nitrogenase (nifH) genes from heterotrophic N2‐fixing (diazotrophic) prokaryotes in unusual habitats challenge the paradigm that pelagic marine N2 fixation is constrained to cyanobacteria in warm, oligotrophic, surface waters. Here, we compare NFR and diazotrophic diversity (assessed via high‐throughput nifH sequencing) from a region known to be dominated by cyanobacterial diazotrophs (the North Pacific Subtropical Gyre, NPSG) to two regions dominated by heterotrophic diazotrophs: the Eastern South Pacific (ESP, from the Chilean upwelling system to the subtropical gyre) and the Pacific Northwest coastal upwelling system (PNW). We observed distinct biogeographical patterns among the three regions. Diazotrophic community structure differed strongly between the NPSG, dominated by cyanobacterium UCYN‐A, and the ESP, dominated by heterotrophic nifH group 1J/1K, yet surface NFR were similar in magnitude (up to 5.1 nmol N L−1 d−1). However, while diverse, predominantly heterotrophic nifH genes were recovered from the PNW and the mesopelagic of the NPSG, NFR were undetectable in both of these environments (although glucose amendments stimulated low rates in the deep NPSG). Our work suggests that while diazotrophs may be nearly omnipresent in marine waters, the activity of this functional group is regionally restricted. Further, we show that the detection limits of the 15N2 fixation assay suggest that many of the low NFR reported for the mesopelagic (often &lt; 0.1 nmol N L−1 d−1 in the literature) are not indicative of active diazotrophy, highlighting the challenges of assessing the ecosystem significance of heterotrophic diazotrophs.

Soil diazotrophic community structure altered in rice crop rotated with mungbean or maize in Cai Lay district, Tien Giang province

Nitrogen availability is often one of the limiting factors for intensive rice (Oryza sativa) cultivation. Rotation of rice with upland crops partially reduces nutrient depletion. This study was carried out at CaiLay district, Tien Giang province with the aim to investigate the effect of alternating the rice crop with maize (Zea mays) and mungbean (Phaseolus aureus)in different rotational systems on the diazotrophic community in soilusing pyrosequencing of the nifH genes. The results showed that the community structure of the diazotroph communities in soils were different when rice crop was alternated with either maize or mungbean crop than that in rice monoculture. The nifH sequences were highly diverse and assigned to eleven bacterial phyla and one Archaeal phylum. Proteobacteria and Firmicutes were the most common phyla carrying the nifH gene. The propotion of the Archaea, Betaproteobacteria, Cyanobacteria, Deltaproteobacteria, Firmicutes, Gammaproteobacteria and Nitrospira was significantly different among the treatments. The relative abundances of Anaeromyxobacter, and Geobacter were greater in RRR than in the RMgR treatment while Heliobacterium and Desulfosporosinus were higher in the RMgR than those in the RRR and RMR treatment.

Environmental Conditions Outweigh Geographical Contiguity in Determining the Similarity of nifH-Harboring Microbial Communities in Sediments of Two Disconnected Marginal Seas.

Ecological evidence suggests that heterotrophic diazotrophs fueled by organic carbon respiration in sediments play an important role in marine nitrogen fixation. However, fundamental knowledge about the identities, abundance, diversity, biogeography, and controlling environmental factors of nitrogen-fixing communities in open ocean sediments is still elusive. Surprisingly, little is known also about nitrogen-fixing communities in sediments of the more research-accessible marginal seas. Here we report on an investigation of the environmental geochemistry and putative diazotrophic microbiota in the sediments of Bohai Sea, an eutrophic marginal sea of the western Pacific Ocean. Diverse and abundant nifH gene sequences were identified and sulfate-reducing bacteria (SRB) were found to be the dominant putative nitrogen-fixing microbes. Community statistical analyses suggested bottom water temperature, bottom water chlorophyll a content (or the covarying turbidity) and sediment porewater Eh (or the covarying pH) as the most significant environmental factors controlling the structure and spatial distribution of the putative diazotrophic communities, while sediment Hg content, sulfide content, and porewater -Si content were identified as the key environmental factors correlated positively with the nifH gene abundance in Bohai Sea sediments. Comparative analyses between the Bohai Sea and the northern South China Sea (nSCS) identified a significant composition difference of the putative diazotrophic communities in sediments between the shallow-water (estuarine and nearshore) and deep-water (offshore and deep-sea) environments, and sediment porewater dissolved oxygen content, water depth and in situ temperature as the key environmental factors tentatively controlling the species composition, community structure, and spatial distribution of the marginal sea sediment nifH-harboring microbiota. This confirms the ecophysiological specialization and niche differentiation between the shallow-water and deep-water sediment diazotrophic communities and suggests that the in situ physical and geochemical conditions play a more important role than geographical contiguity in determining the community similarity of the diazotrophic microbiota in marginal sea sediments.

Biogeographic patterns of soil diazotrophic communities across six forests in North America.

Soil diazotrophs play important roles in ecosystem functioning by converting atmospheric N2 into biologically available ammonium. However, the diversity and distribution of soil diazotrophic communities in different forests and whether they follow biogeographic patterns similar to macroorganisms still remain unclear. By sequencing nifH gene amplicons, we surveyed the diversity, structure and biogeographic patterns of soil diazotrophic communities across six North American forests (126 nested samples). Our results showed that each forest harboured markedly different soil diazotrophic communities and that these communities followed traditional biogeographic patterns similar to plant and animal communities, including the taxa-area relationship (TAR) and latitudinal diversity gradient. Significantly higher community diversity and lower microbial spatial turnover rates (i.e. z-values) were found for rainforests (~0.06) than temperate forests (~0.1). The gradient pattern of TARs and community diversity was strongly correlated (r(2) >0.5) with latitude, annual mean temperature, plant species richness and precipitation, and weakly correlated (r(2) <0.25) with pH and soil moisture. This study suggests that even microbial subcommunities (e.g. soil diazotrophs) follow general biogeographic patterns (e.g. TAR, latitudinal diversity gradient), and indicates that the metabolic theory of ecology and habitat heterogeneity may be the major underlying ecological mechanisms shaping the biogeographic patterns of soil diazotrophic communities.

Diazotroph community structure in the deep oxygen minimum zone of the Costa Rica Dome.

Oxygen minimum zones (OMZs), characterized by depleted dissolved oxygen concentration in the intermediate depth of the water column, are predicted to expand under the influence of global warming. Recent studies in the Eastern Tropical South Pacific Ocean and Arabian Sea have reported that heterotrophic nitrogen fixation is active in the OMZs. In this study, we investigated the community structure of diazotrophs in the OMZ of the Costa Rica Dome (CRD) upwelling region in the Eastern Tropical North Pacific Ocean, using 454-pyrosequencing of nifH gene amplicons. Comparing diazotroph assemblages in different depth strata of the OMZ (200-1000 m in depth), we found a unique diazotroph community in the OMZ core, which was mainly dominated by methanotroph-like diazotrophs, suggesting a potential coupling of nitrogen cycle and methane assimilation. In addition, some OTUs revealed in this study, especially those belonging to the large sub-cluster Vibrio diazotrophicus, were reported to be abundant and expressing the nifH gene in other OMZs. Our results suggest that the unique hydrographic conditions in OMZs may support similar assemblages of diazotrophs, and heterotrophic nitrogen fixation could also be occurring in our studied region. Our study provides the first insight into the composition and distribution of putative diazotrophs in the CRD OMZ.

亚热带分层水库固氮微生物时空分布格局

PDF HTML阅读 XML下载 导出引用 引用提醒 亚热带分层水库固氮微生物时空分布格局 DOI: 10.5846/stxb201504250854 作者: 作者单位: 中国科学院城市环境研究所 城市环境与健康重点实验室 水生态健康研究组,中国科学院城市环境研究所 城市环境与健康重点实验室 水生态健康研究组,中国科学院城市环境研究所 城市环境与健康重点实验室 水生态健康研究组,中国科学院城市环境研究所 城市环境与健康重点实验室 水生态健康研究组,中国科学院城市环境研究所 城市环境与健康重点实验室 水生态健康研究组 作者简介: 通讯作者: 中图分类号: 基金项目: 国家自然科学基金项目（31370471，31172114）；福建省杰出青年科学基金项目（2012J06009） Spatiotemporal patterns of diazotrophic microorganisms in a subtropical stratified reservoir Author: Affiliation: Aquatic Ecohealth Group,Key Laboratory of Urban Environment and Health,Institute of Urban Environment,Chinese Academy of Sciences,Aquatic Ecohealth Group,Key Laboratory of Urban Environment and Health,Institute of Urban Environment,Chinese Academy of Sciences,Aquatic Ecohealth Group,Key Laboratory of Urban Environment and Health,Institute of Urban Environment,Chinese Academy of Sciences,Aquatic Ecohealth Group,Key Laboratory of Urban Environment and Health,Institute of Urban Environment,Chinese Academy of Sciences,Aquatic Ecohealth Group,Key Laboratory of Urban Environment and Health,Institute of Urban Environment,Chinese Academy of Sciences Fund Project: 摘要 | 图/表 | 访问统计 | 参考文献 | 相似文献 | 引证文献 | 资源附件 | 文章评论 摘要:生物固氮作用是水生态系统氮元素的重要来源途径之一，通常通过固氮微生物实现。但是，目前人们对亚热带分层水库固氮微生物多样性、分布和丰度认识还非常有限。以厦门市汀溪水库为例，基于固氮基因（nifH）综合应用克隆文库、定量PCR、定量RT-PCR研究固氮微生物在不同季节和不同水层的时空分布格局与演替规律。结果表明，汀溪水库具有丰富多样的固氮微生物，包括蓝藻、α-变形菌、β-变形菌、γ-变形菌、厚壁菌，以及少量未知的固氮细菌和序列；固氮微生物的群落组成、丰度、多样性和活性均呈现显著的时空差异。春、夏和秋3季表层和底层蓝藻nifH基因序列所占比例均超过50%，其中表层高于底层；冬季表层和底层蓝藻OTU数目比例超过50%。聚类分析表明，冬季表层和底层群落汇聚为一类；春、夏和秋三个季节表层首先聚为一类，然后与底层分别汇为一支。汀溪水库热分层时期的固氮微生物群落组成的空间差异大于季节差异，而且表层水体蓝藻在所有固氮微生物中占据绝对优势地位。相关分析表明，固氮微生物RNA丰度和RNA/DNA分别与氨氮、水温显著负相关；固氮微生物DNA丰度与溶解氧、pH、叶绿素a显著负相关，与硝氮显著正相关。综上所述，亚热带水库热分层对固氮微生物的群落结构具有显著的影响，在水库环境保护和生态管理中，特别是蓝藻水华防控时，要充分考虑水体热分层的生态效应。 Abstract:Biological nitrogen fixation, which is mediated by nitrogen-fixing microorganisms (diazotrophs), is an important source of fixed nitrogen in aquatic ecosystems. Recent advances in molecular biology techniques are leading to progress in the elucidation of the diazotrophic community possessing the nifH nitrogenase gene in various ecosystems. So far, the majority of studies of diazotrophic communities are based on marine samples, with freshwater habitats remaining largely unexplored. The aims of this study are to characterize the spatiotemporal patterns of a diazotrophic microbial community in a subtropical stratified reservoir (Tingxi Reservoir, southeast China), and to examine the relationships between the diazotrophic community structure and environmental variables. In this study, samples from the water column (five layers) were collected in July and October 2012, and in January and April 2013. Nitrogen-fixing microorganisms were studied using quantitative real-time PCR and clone library techniques. In Tingxi Reservoir, the water column was well mixed in winter, whereas there was clear and stable stratification in spring, summer, and autumn. Our results indicated that there were distinct spatial and seasonal patterns of abundance, activity, composition, and diversity in the diazotrophic community that was linked to water stratification in the Tingxi Reservoir. In total, 106 OTUs belonging to seven groups (i.e., 46 Cyanobacteria, 21 α-Proteobacteria, 3 β-Proteobacteria, 9 γ-Proteobacteria, 1 Firmicutes, 18 unidentified nitrogen-fixing bacteria, and 8 unknown taxa) were observed, the most diverse and dominant group of which was cyanobacteria. Both α- and γ-proteobacteria were much more common than β-proteobacteria in the reservoir.The deeper waters harbored a high percentage of unidentified bacteria and unknown taxa. The number of sequences similar to cyanobacteria in the surface water was higher than in the bottom water in spring, summer, and autumn. The Cyanobacteria OTUs number contributed more than 50% of the total OTUs in both surface and bottom waters in winter. Firmicutes were only detected in the surface water sample in October. Interestingly, our cluster analysis indicated that surface water diazotrophic communities in spring, summer, and autumn (with a stable stratification) first formed a group, then clustered with the bottom communities. However, both surface and bottom diazotrophic communities exhibited a relatively high similarity in winter due to water mixing. The pH, dissolved oxygen, and chlorophyll a showed a significant negative relationship with the DNA copy number, whereas the NOx-N showed a strong positive correlation with the DNA copy number. Water temperature and NH4-N had a negative significant relationship with RNA/DNA ratio and RNA copy number, respectively. It appeared that nitrogen-fixing bacteria showed distinctly nonrandom spatial and seasonal distributions in the Tingxi Reservoir, and their communities were either complexly structured by the thermal stratification or adapted to different environmental niches. Therefore, a stratification-based management strategy should be considered when developing methods for protecting drinking water quality and for controlling the cyanobacterial blooms. 参考文献 相似文献 引证文献

Temporal variation of diazotrophic community abundance and structure in surface and subsoil under four fertilization regimes during a wheat growing season

Biological nitrogen fixation (BNF) is an initial process of the nitrogen cycle (Cleveland et al., 1999) by the specialized microorganisms known as diazotroph. However, little information is available concerning the dynamic changes of diazotrophic communities in surface and subsoil layers. In this study, five representative season soil samples were collected from surface (0–20cm) and subsoil (20–40cm) in the long term experimental field plots that received no nitrogen fertilizer (CK), chemical fertilizers (CF), organic-inorganic mixed fertilizer (OIMF) and organic fertilizer (OF) since 2005. Real-time PCR was used to determine the nifH and total bacterial 16S rRNA gene abundance. Terminal restriction fragment length polymorphism (T-RFLP) of nifH gene was used to analyze the changes of diazotrophic communities. Results revealed that the abundance of nifH and 16S rRNA genes declined with increased soil depth regardless of fertilization regimes, although considerably high abundance was also observed in subsoils. The abundance of nifH genes was significantly positively correlated with the total bacterial abundance in oligotrophic subsoil layers, but not in the topsoil. Ammonium contents showed significant correlation to the nifH gene abundance in both surface and subsoil. Clustering analysis of the T-RFLP profiles showed that diazotrophic structures were clearly separated by surface and subsoil habitats. Permutational multivariate analyses demonstrated that soil depth, rather than the sampling time or fertilization regime, was the important factor that influence the diazotrophic structures. In the surface soil, soil organic carbon (SOC) and ammonium contents were significantly positively correlated to the diazotrophic community structures. These results suggest soil physiochemical properties selected for distinct diazotrophic communities inhabit in the topsoil and subsoil.