Variation in the nitrous oxide reductase gene (nosZ)-denitrifying bacterial community in different primary succession stages in the Hailuogou Glacier retreat area, China

Background: The Hailuogou Glacier in the Gongga Mountain region (SW China), on the southeastern edge of the Tibetan Plateau, is well known for its low-elevation modern glaciers. Since the end of the Little Ice Age (LIA), the Hailuogou Glacier has retreated continuously due to global warming, primary vegetation succession and soil chronosequence have developed in this retreat area. The retreated area of Hailuogou Glacier has not been strongly disturbed by human activities, thus it is an ideal models for exploring the biological colonization of nitrogen in the primary successional stages of ecosystem. The nosZ gene encodes the catalytic center of nitrous oxide reductase and is an ideal molecular marker in studying the variation in the denitrifying bacterial community. Methods: Soil properties as well as abundance and composition of the denitrifying bacterial community were determined via chemical analysis, quantitative polymerase chain reaction (qPCR), and terminal restriction fragment length polymorphism (T-RFLP), respectively. The relationships between the nosZ denitrifying bacterial community and soil properties were determined using redundancy analysis (RDA). Soil properties, potential denitrify activity (PDA), and the nitrous oxide reductase gene (nosZ)-denitrifying bacterial communities significantly differed among successional stages. Results: Soil properties, potential denitrify activity (PDA), and the nitrous oxide reductase gene (nosZ)-denitrifying bacterial communities significantly differed among successional stages. Soil pH in the topsoil decreased from 8.42 to 7.19 in the course of primary succession, while soil organic carbon (SOC) and total nitrogen (TN) gradually increased with primary succession. Available phosphorus (AP) and available potassium (AK), as well as potential denitrify activity (PDA), increased gradually and peaked at the 40-year-old site. The abundance of the nosZ denitrifying bacterial community followed a similar trend. The variation in the denitrifying community composition was complex; Mesorhizobium dominated the soil in the early successional stages (0-20 years) and in the mature phase (60 years), with a relative abundance greater than 55%. Brachybacterium was increased in the 40-year-old site, with a relative abundance of 62.74%, while Azospirillum dominated the early successional stages (0-20 years). Redundancy analysis (RDA) showed that the nosZ denitrifying bacterial community correlated with soil available phosphorus and available potassium levels (P < 0.01).

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Variation in the nitrous oxide reductase gene (nosZ)-denitrifying bacterial community in different primary succession stages in the Hailuogou Glacier retreat area, China

10.7287/peerj.preprints.27481v1 ◽

2019 ◽

Author(s):

Yan Bai ◽

Xiying Huang ◽

Xiangrui Zhou ◽

Quanju Xiang ◽

Ke Zhao ◽

...

Keyword(s):

Nitrous Oxide ◽

Bacterial Community ◽

Soil Properties ◽

Bacterial Communities ◽

Redundancy Analysis ◽

Primary Succession ◽

Available Phosphorus ◽

Nitrous Oxide Reductase ◽

Reductase Gene ◽

Successional Stages

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Effects of Nitrogen Input on Community Structure of the Denitrifying Bacteria with Nitrous Oxide Reductase Gene (nosZ I): A Long-Term Pond Experiment

10.21203/rs.3.rs-1145044/v1 ◽

2021 ◽

Author(s):

Jing Zhou ◽

Yong Kong ◽

Mengmeng Wu ◽

Fengyue Shu ◽

Haijun Wang ◽

...

Keyword(s):

Nitrous Oxide ◽

Bacterial Communities ◽

Denitrifying Bacteria ◽

Nitrous Oxide Reductase ◽

Public Attention ◽

Reductase Gene ◽

N Input ◽

Denitrifying Microorganisms ◽

N Loading

Abstract Excessive nitrogen (N) input is an important factor influencing aquatic ecosystems and has received increasing public attention in the past decades. It remains unclear, however, how N input affects the denitrifying bacterial communities that play a key role in regulating N cycles in various ecosystems. To test our hypothesis – that the abundance and biodiversity of denitrifying bacterial communities decrease with increasing N – we compared the abundance and composition of denitrifying bacteria having nitrous oxide reductase gene (nosZ I) from sediments (0-20 cm) in five experimental ponds with different nitrogen fertilization treatment (TN10, TN20, TN30, TN40, TN50) using quantitative PCR and pyrosequencing techniques. We found that: 1) N addition significantly decreased nosZ I gene abundance, 2) the Invsimpson and Shannon indices (reflecting biodiversity) first increased significantly along with the increasing N loading in TN10~TN40 followed by a decrease in TN50, 3) the beta diversity of the nosZ I denitrifier was clustered into three groups along the TN concentration levels: Cluster I (TN50), Cluster II (TN40), and Cluster III (TN10-TN30), 4) the proportions of Alphaproteobacteria and Betaproteobacteria in the high-N treatment (TN50) were significantly lower than in the lower N treatments (TN10-TN30). 5). The TN concentration was the most important factor driving the alteration of denitrifying bacteria assemblages. Our findings shed new light on the response of denitrification-related bacteria to long-term N loading at pond scale and on the response of denitrifying microorganisms to N pollution.

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Variation in denitrifying bacterial communities along a primary succession in the Hailuogou Glacier retreat area, China

PeerJ ◽

10.7717/peerj.7356 ◽

2019 ◽

Vol 7 ◽

pp. e7356

Author(s):

Yan Bai ◽

Xiying Huang ◽

Xiangrui Zhou ◽

Quanju Xiang ◽

Ke Zhao ◽

...

Keyword(s):

Microbial Communities ◽

Community Composition ◽

Bacterial Communities ◽

Primary Succession ◽

Abiotic Factors ◽

Bacterial Community Composition ◽

Living Environment ◽

Available Phosphorus ◽

The Tibetan Plateau ◽

Successional Stages

Background The Hailuogou Glacier is located at the Gongga Mountain on the southeastern edge of the Tibetan Plateau, and has retreated continuously as a result of global warming. The retreat of the Hailuogou Glacier has left behind a primary succession along soil chronosequences. Hailuogou Glacier’s retreated area provides an excellent living environment for the colonization of microbes and plants, making it an ideal model to explore plant successions, microbial communities, and the interaction of plants and microbes during the colonization process. However, to date, the density of the nitrogen cycling microbial communities remain unknown, especially for denitrifiers in the primary succession of the Hailuogou Glacier. Therefore, we investigated the structural succession and its driving factors for denitrifying bacterial communities during the four successional stages (0, 20, 40, and 60 years). Methods The diversity, community composition, and abundance of nosZ-denitrifiers were determined using molecular tools, including terminal restriction fragment length polymorphism and quantitative polymerase chain reactions (qPCR). Results nosZ-denitrifiers were more abundant and diverse in soils from successional years 20–60 compared to 0–5 years, and was highest in Site3 (40 years). The denitrifying bacterial community composition was more complex in older soils (40–60 years) than in younger soils (≤20 years). The terminal restriction fragments (T-RFs) of Azospirillum (90 bp) and Rubrivivax (95 bp) were dominant in soisl during early successional stages (0–20 years) and in the mature phase (40–60 years), respectively. Specific T-RFs of Bradyrhizobium (100 bp) and Pseudomonas (275 bp) were detected only in Site3 and Site4, respectively. Moreover, the unidentified 175 bp T-RFs was detected only in Site3. Of the abiotic factors that were measured in this study, soil available phosphorus, available potassium and denitrifying enzyme activity (DEA) correlated significantly with the community composition of nosZ-denitrifiers (P < 0.05 by Monte Carlo permutation test within RDA analysis).

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Effect of straw biochar amendment on tobacco growth, soil properties, and rhizosphere bacterial communities

Scientific Reports ◽

10.1038/s41598-021-00168-y ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Jiayu Zheng ◽

Jixu Zhang ◽

Lin Gao ◽

Rui Wang ◽

Jiaming Gao ◽

...

Keyword(s):

Bacterial Community ◽

Soil Properties ◽

Bacterial Communities ◽

Agronomic Traits ◽

Diversity Indices ◽

Community Diversity ◽

High Dose ◽

Rhizosphere Soils ◽

Tobacco Growth ◽

Biochar Amendment

AbstractBiochar is an effective soil conditioner. However, we have limited understanding of biochar effects on the tobacco growth and bacterial communities in rhizosphere. The aim of this study was to investigate the effects of different straw biochar amendment (0, 2, 10, and 50 g/kg dry soil) on tobacco growth, soil properties, and bacterial communities in rhizosphere by pot trials. Most of tobacco agronomic traits increased when the application rate varied from 0 to 10 g/kg, but were inhibited by 50 g/kg of biochar application. Soil pH, SOC, available nutrients and soil urease, invertase, and acid phosphatase activities were all increased with the biochar application, whereas catalase activity decreased or remained unchanged. The OTUs and bacterial community diversity indices differed with the biochar application doses in rhizosphere and non-rhizosphere soils. And significant differences in bacterial communities were found between the rhizosphere and non-rhizosphere soils despite the biochar addition. Firmicutes, Proteobacteria, Acidobacteria, Bacteroidetes, and Actinobacteria were the dominant phyla in all soil samples, but they had different abundances in different treatment influenced by the rhizosphere and biochar effect. The high dose of biochar (50 g/kg) decreased the similarity of soil bacterial community structure in rhizosphere compared with those in non-rhizosphere soil. These results provide a better understanding of the microecological benefits of straw biochar in tobacco ecosystem.

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Bacterial Communities in the Rhizosphere and Phyllosphere of Halophytes and Drought-Tolerant Plants in Mediterranean Ecosystems

Microorganisms ◽

10.3390/microorganisms8111708 ◽

2020 ◽

Vol 8 (11) ◽

pp. 1708

Author(s):

Savvas Genitsaris ◽

Natassa Stefanidou ◽

Kleopatra Leontidou ◽

Theodora Matsi ◽

Katerina Karamanoli ◽

...

Keyword(s):

Bacterial Community ◽

Soil Properties ◽

Bacterial Communities ◽

Mediterranean Ecosystems ◽

Community Diversity ◽

Sampling Location ◽

Rrna Gene ◽

Sodic Soils ◽

Drought Tolerant ◽

Tolerant Plants

The aim of the study was to investigate the bacterial community diversity and structure by means of 16S rRNA gene high-throughput amplicon sequencing, in the rhizosphere and phyllosphere of halophytes and drought-tolerant plants in Mediterranean ecosystems with different soil properties. The locations of the sampled plants included alkaline, saline-sodic soils, acidic soils, and the volcanic soils of Santorini Island, differing in soil fertility. Our results showed high bacterial richness overall with Proteobacteria and Actinobacteria dominating in terms of OTUs number and indicated that variable bacterial communities differed depending on the plant’s compartment (rhizosphere and phyllosphere), the soil properties and location of sampling. Furthermore, a shared pool of generalist bacterial taxa was detected independently of sampling location, plant species, or plant compartment. We conclude that the rhizosphere and phyllosphere of native plants in stressed Mediterranean ecosystems consist of common bacterial assemblages contributing to the survival of the plant, while at the same time the discrete soil properties and environmental pressures of each habitat drive the development of a complementary bacterial community with a distinct structure for each plant and location. We suggest that this trade-off between generalist and specialist bacterial community is tailored to benefit the symbiosis with the plant.

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Bacterial communities in paddy soil and ditch sediment under rice-crab co-culture system

AMB Express ◽

10.1186/s13568-021-01323-4 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Xu Jiang ◽

Hui Ma ◽

Qing-lei Zhao ◽

Jun Yang ◽

Cai-yun Xin ◽

...

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Relative Abundance ◽

Paddy Soil ◽

Bacterial Communities ◽

Bacterial Community Structure ◽

High Throughput Sequencing ◽

Available Phosphorus ◽

Uncultured Bacterium ◽

Ditch Sediment

AbstractAs an important form of sustainable agriculture, rice-crab (Eriocheir sinensis) co-culture is rapid developing worldwide. However, the knowledge on the bacterial communities of the different components of the system is limited. In this study, we investigated the bacterial community structure in paddy soil and ditch sediment by using high-throughput sequencing technology. The results showed that compared with the ditch sediment, the content of NH4+-N in paddy soil decreased by 62.31%, and the content of AP (available phosphorus) increased by 172.02% (P < 0.05). The most abundant phyla in paddy soil and ditch sediment were Proteobacteria, Bacteroidetes and Chloroflexi, whose relative abundance was above 65%. Among the dominant genera, the relative abundance of an uncultured bacterium genus of Saprospiraceae and an uncultured bacterium genus of Lentimicrobiaceae in paddy soil was significantly lower than ditch sediment (P < 0.05). Alpha diversity indicated that the bacterial diversity of paddy soil and ditch sediment was similar. The bacterial community structure was affected by the relative abundance of bacteria, not the species of bacteria. Redundancy analysis (RDA) showed that the bacterial communities in paddy soil and ditch sediment were correlated with physicochemical properties. Our findings showed that the bacterial community structure was distinct in paddy soil and ditch sediment under rice-crab co-culture probably due to their different management patterns. These results can provide theoretical support for improving rice-crab co-culture technology.

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Absence of the Nitrous Oxide Reductase Gene Cluster in Commercial Alfalfa Inoculants Is Probably Due to the Extensive Loss of Genes During Rhizobial Domestication

Microbial Ecology ◽

10.1007/s00248-018-1145-9 ◽

2018 ◽

Vol 76 (2) ◽

pp. 299-302 ◽

Cited By ~ 3

Author(s):

Silvina Brambilla ◽

Romina Frare ◽

Gabriela Soto ◽

Cintia Jozefkowicz ◽

Nicolás Ayub

Keyword(s):

Nitrous Oxide ◽

Gene Cluster ◽

Nitrous Oxide Reductase ◽

Reductase Gene

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Nitrous oxide reductase gene (nosZ) and N2O reduction along the littoral gradient of a eutrophic freshwater lake

Journal of Environmental Sciences ◽

10.1016/s1001-0742(12)60005-9 ◽

2013 ◽

Vol 25 (1) ◽

pp. 44-52 ◽

Cited By ~ 19

Author(s):

Chaoxu Wang ◽

Guibing Zhu ◽

Yu Wang ◽

Shanyun Wang ◽

Chengqing Yin

Keyword(s):

Nitrous Oxide ◽

Freshwater Lake ◽

Nitrous Oxide Reductase ◽

N2o Reduction ◽

Reductase Gene

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Temporal and Spatial Characterization of Sediment Bacterial Communities From Lake Wetlands in a Plain River Network Region

10.21203/rs.3.rs-1042496/v1 ◽

2021 ◽

Author(s):

Wei Huang ◽

Chengqi Tu ◽

Zhenghai Jin ◽

Haoran Yang ◽

Changyu Lu ◽

...

Keyword(s):

Bacterial Community ◽

Bacterial Communities ◽

Redundancy Analysis ◽

Diversity Index ◽

Critical Role ◽

Rrna Gene ◽

Linear Discriminant ◽

Different Seasons ◽

Lake Wetlands ◽

Sediment Bacterial Communities

Abstract Sediment bacterial communities are a vital component of microbial communities in aquatic and terrestrial ecosystems and they play a critical role in lake wetlands. To investigate the effect of season, depth and regional environmental factors on the composition and diversity of bacterial communities in lake wetland sediments, the millions of Illumina reads (16S rRNA gene amplicons) from sediment bacterial communities in different seasons were examined using a technically consistent approach. Results from diversity index, relative abundance, principal component analysis (PCA), redundancy analysis (RDA) and linear discriminant analysis effect size (LEfSe) analysis indicated that the diversity of the bacterial community in summer was generally higher than in other seasons. Proteobacteria was the most abundant phylum in the sediment samples in different seasons (43.15%–57.41%) and different layers (39.66%–77.97%); the autumn sediments were enriched with Firmicutes (5.67%) and Chloroflexi (12.5%); in all four seasons the sediments were enriched with Betaproteobacteria (14.98%–23.45%), Gammaproteobacteria (11.98%–14.36%) and Deltaproteobacteria (8.68%–14.45%). In the bottom sediments (10–25 cm) Chloroflexi were abundant (average value 10.42%), while Bacteroidetes was the dominant phylum in the surface sediments; and redundancy analysis found that total phosphorus (TP) (P = 0.036) was the main environmental factor influencing the sediment bacterial community in different layers. This study provides a reference for further understanding the effects of seasonal changes on sediment microorganisms in lake wetlands.

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Effects of fertilisation on microbial communities in short-term coal mine reclamation

Soil Research ◽

10.1071/sr19262 ◽

2020 ◽

Vol 58 (8) ◽

pp. 779

Author(s):

Jian Zhang ◽

Yinghe Xie ◽

Ying Wei ◽

Huisheng Meng ◽

Yanzhuan Cao ◽

...

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Soil Properties ◽

Coal Mining ◽

Coal Mine ◽

Bacterial Communities ◽

Community Diversity ◽

Short Term ◽

Beneficial Effects

The recovery of the belowground microbial community structure and diversity that occurs in long-term coal mining reclamation is critical to reclamation success. However, long-term coal mining reclamation can take ~10–30 years. Therefore, finding an effective method for promoting coal mine soil restoration in the short-term is necessary to minimise reclamation time. This study investigated the response of soil bacterial communities to fertilisation along a chronosequence of short-term reclamation. Fertilised and unfertilised soils with three short-term reclamation stages were examined to characterise soil properties, as well as bacterial structure and diversity. Fertilisation promoted available nitrogen, phosphate, potassium, and soil organic matter, as well as benefits in bacterial community diversity across the three stages, with the most beneficial effects at 7 years. 16S rRNA sequencing data showed that the predominant phyla across all soils were Proteobacteria, Actinobacteria, Acidobacteria, Bacteroidetes, Chloroflexi, and Gemmatimonadetes. Abundance of each phylum was altered by reclamation time and fertilisation. Clustering and functional analysis indicated that the bacterial community structure in soils with a longer reclamation time was more similar to that in natural soils, suggesting that longer reclamation resulted in increased soil activity and bacterial community diversity, which is likely also true for fertilisation. Our results demonstrate that reclamation duration is the main driving force to recover soil properties and bacterial communities, and fertilisation could enhance the beneficial effects with longer reclamation duration. Therefore, short-term reclamation, combined with fertiliser, is a potential strategy to improve soil conditions in coal mine areas and shorten the recovery time of reclaimed soils.

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