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With the development of economics, the deposition of available nitrogen in the terrestrial ecosystem is increasing dramatically due to anthropic activities, which negatively impacts the sustainability of the ecosystem ecology. In this study, the effect of long-term stimulated nitrogen deposition[with nitrogen addition of 0, 1, 4, 8, and 32 g·(m 2 ·a) -1 ] on the microbial community structure of soil was investigated in a temperate steppe in Inner Mongolia using a pyrosequencing technique targeting the bacterial 16S rRNA gene. The results show that the available nitrogen in soil increases with increasing nitrogen addition, resulting in the decrease of the soil pH. The results of pyrosequencing indicate that soil bacterial OTU (operational taxonomy unit) numbers increase with increasing nitrogen deposition, while bacterial α diversity indices show an initial increase and subsequent decrease. Non-metric multidimensional scaling (NMDS) analysis indicates that the bacterial community structure significantly varies among treatments, which can be largely attributed to the changes in the soil pH and nitrogen content due to nitrogen deposition. At the class level, the relative abundance of different bacterial groups shows a varying trend depending on the nitrogen deposition. This study indicates that long-term nitrogen deposition significantly impacts the bacterial community by changing the soil properties.

Terrestrial-marine boundaries are significant sites of biogeochemical activity with delineated gradients from land to sea. While niche differentiation of ammonia-oxidizing archaea (AOA) and bacteria (AOB) driven by pH and nitrogen is well known, the patterns and environmental drivers of AOA and AOB community structure and activity across soil-sediment boundaries have not yet been determined. In this study, nitrification potential rate, community composition and transcriptional activity of AOA and AOB in soil, soil/sediment interface and sediments of two coastal Bays were characterized using a combination of field investigations and microcosm incubations. At DNA level, amoA gene abundances of AOA were significantly greater than AOB in soil, while in sediments AOB were significantly more abundant than AOA, but at the soil/sediment interface there were equal numbers of AOA and AOB amoA genes. Microcosm incubations provided further evidence, through qPCR and DGGE-sequencing analysis of amoA transcripts, that AOA were active in soil, AOB in sediment and both AOA and AOB were active at the soil/sediment interface. The AOA and AOB community composition shifted across the coastal soil-interface-sediment gradient with salinity and pH identified as major environmental drivers., (© 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.)

Soil ammonia oxidizers, as key players for the ammonia oxidation process in soil N cycling, could respond, adapt, and give feedback to global change. In this research, soil samples were collected from a long-term field experiment with increased precipitation and warming in a temperate steppe of Inner Mongolia. We analyzed the responses of the abundance, diversity, and community structure of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) to warming and increased precipitation using quantitative real-time PCR, terminal restriction fragment length polymorphism (T-RFLP), and clone library. The results showed that increased precipitation significantly stimulated soil pH and warming significantly reduced soil respiration (SR). No significant difference was detected regarding the abundances of amoA genes across all treatments, whereas increased precipitation significantly affected the community structure of soil AOB. However, the interactive effect between warming and increased precipitation had no significant influence on the community structure of soil ammonia oxidizers. The result of the structural equation model indicated that the plant diversity and community structures of soil ammonia oxidizers were significantly correlated, suggesting that there were certain relationships among climate change, microbes, and plants. In conclusion, this study confirmed that soil microorganisms had the ability to adapt to climate change, which could provide important information for predicting future changes in ecosystems.

Dry-rewetting (DW) disturbance frequently occurs in soils due to rainfall and irrigation, and the frequency of DW cycles might exert significant influences on soil microbial communities and their mediated functions. However, how microorganisms respond to DW alternations in soils with a history of heavy metal pollution remains largely unknown. Here, soil laboratory microcosms were constructed to explore the impacts of ten DW cycles on the soil microbial communities in two contrasting soils (fluvo-aquic soil and red soil) under three copper concentrations (zero, medium and high). Results showed that the fluctuations of substrate induced respiration (SIR) decreased with repeated cycles of DW alternation. Furthermore, the resistance values of substrate induced respiration (RS-SIR) were highest in non-copper-stressed (zero) soils. Structural equation model (SEM) analysis ascertained that the shifts of bacterial communities determined the changes of RS-SIR in both soils. The rate of bacterial community variance was significantly lower in non-copper-stressed soil compared to the other two copper-stressed (medium and high) soils, which might lead to the higher RS-SIR in the fluvo-aquic soil. As for the red soil, the substantial increase of the dominant group WPS-2 after DW disturbance might result in the low RS-SIR in the high copper-stressed soil. Moreover, in both soils, the bacterial diversity was highest in non-copper-stressed soils. Our results revealed that initial copper stress could decrease the resistance of soil microbial community structure and function to subsequent DW disturbance., (Copyright © 2015. Published by Elsevier B.V.)

Unraveling the distribution patterns of plants and animals along the elevational gradients has been attracting growing scientific interests of ecologists, whether the microbial communities exhibit similar elevational patterns, however, remains largely less documented. Here, we investigate the biogeographic distribution of soil archaeal and bacterial communities across three vertical climate zones (3,106-4,479 m.a.s.l.) in Mt. Shegyla on the Tibetan Plateau, by combining quantitative PCR and high-throughput barcoded pyrosequencing approaches. Our results found that the ratio of bacterial to archaeal 16S rRNA gene abundance was negatively related with elevation. Acidobacteria dominated in the bacterial communities, Marine benthic group A dominated in the archaeal communities, and the relative abundance of both taxa changed significantly with elevation. At the taxonomic levels of domain, phylum, and class, more bacterial taxa than archaeal exhibited declining trend in diversity along the increasing elevational gradient, as revealed by Shannon and Faith's phylogenetic diversity indices. Unweighted UniFrac distance clustering showed that the bacterial communities from the mountainous temperate zone clustered together, whereas those from the subalpine cool temperate zone clustered together. However, the partitioning effect of elevational zones on the archaeal community was much weaker compared to that on bacteria. Redundancy analysis revealed that soil geochemical factors explained 58.3 % of the bacterial community variance and 75.4 % of the archaeal community variance. Taken together, we provide evidence that soil bacteria exhibited more apparent elevational zonation feature and decreased diversity pattern than archaea with increasing elevation, and distribution patterns of soil microbes are strongly regulated by soil properties along elevational gradient in this plateau montane ecosystem.

Mercury (Hg) pollution is usually regarded as an environmental stress in reducing microbial diversity and altering bacterial community structure. However, these results were based on relatively short-term studies, which might obscure the real response of microbial species to Hg contamination. Here, we analysed the bacterial abundance and community composition in paddy soils that have been potentially contaminated by Hg for more than 600 years. Expectedly, the soil Hg pollution significantly influenced the bacterial community structure. However, the bacterial abundance was significantly correlated with the soil organic matter content rather than the total Hg (THg) concentration. The bacterial alpha diversity increased at relatively low levels of THg and methylmercury (MeHg) and subsequently approached a plateau above 4.86 mg kg(-1) THg or 18.62 ng g(-1) MeHg, respectively. Contrasting with the general prediction of decreasing diversity along Hg stress, our results seem to be consistent with the intermediate disturbance hypotheses with the peak biological diversity under intermediate disturbance or stress. This result was partly supported by the inconsistent response of bacterial species to Hg stress. For instance, the relative abundance of Nitrospirae decreased, while that of Gemmatimonadetes increased significantly along the increasing soil THg and MeHg concentrations. In addition, the content of SO(4)(2-), THg, MeHg and soil depth were the four main factors influencing bacterial community structures based on the canonical correspondence analysis (CCA). Overall, our findings provide novel insight into the distribution patterns of bacterial community along the long-term Hg-contaminated gradient in paddy soils.

Methylated arsenic (As) species are a common constituent of rice grains accounting for 10-90% of the total As. Recent studies have shown that higher plants are unlikely to methylate As in vivo suggesting that As methylation is a microbial mediated process that occurs in soils prior to plant uptake. In this study, we designed primers according to the conserved essential amino acids and structural motifs of arsenite S-adenosylmethionine methyltransferase (ArsM). We report for the first time the successful amplification of the prokaryotic arsM gene in 14 tested soils with wide ranging As concentrations. The abundance and diversity of the arsM gene in the rice rhizosphere soil and roots were analyzed using the designed primers. Results showed that microbes containing arsM genes were phylogenetically diverse, as revealed by the clone library and terminal restriction fragment length polymorphism (T-RFLP) analysis, and were branched into various phyla. Concentration of methylated As species in the soil solution was elevated in the rhizosphere soil and also by the addition of rice straw into the paddy soil, corresponding to the elevated abundance of the arsM gene in the soil. These results, together with evidence of horizontal gene transfer (HGT) of the arsM gene, suggest the genes encoding ArsM in soils are widespread. These findings demonstrate why most rice, when compared with other cereals, contains unusually high concentrations of methylated As species.

Increasing evidence demonstrated the involvement of ammonia-oxidizing archaea (AOA) in the global nitrogen cycle, but the relative contributions of AOA and ammonia-oxidizing bacteria (AOB) to ammonia oxidation are still in debate. Previous studies suggest that AOA would be more adapted to ammonia-limited oligotrophic conditions, which seems to be favored by protonation of ammonia, turning into ammonium in low-pH environments. Here, we investigated the autotrophic nitrification activity of AOA and AOB in five strongly acidic soils (pH<4.50) during microcosm incubation for 30 days. Significantly positive correlations between nitrate concentration and amoA gene abundance of AOA, but not of AOB, were observed during the active nitrification. (13)CO(2)-DNA-stable isotope probing results showed significant assimilation of (13)C-labeled carbon source into the amoA gene of AOA, but not of AOB, in one of the selected soil samples. High levels of thaumarchaeal amoA gene abundance were observed during the active nitrification, coupled with increasing intensity of two denaturing gradient gel electrophoresis bands for specific thaumarchaeal community. Addition of the nitrification inhibitor dicyandiamide (DCD) completely inhibited the nitrification activity and CO(2) fixation by AOA, accompanied by decreasing thaumarchaeal amoA gene abundance. Bacterial amoA gene abundance decreased in all microcosms irrespective of DCD addition, and mostly showed no correlation with nitrate concentrations. Phylogenetic analysis of thaumarchaeal amoA gene and 16S rRNA gene revealed active (13)CO(2)-labeled AOA belonged to groups 1.1a-associated and 1.1b. Taken together, these results provided strong evidence that AOA have a more important role than AOB in autotrophic ammonia oxidation in strongly acidic soils.

Eukaryota, bacteria and archaea are the three domains of life. As the third domain of life, archaea has been found not only in extreme environments such as high-temperature, high-saline, and extremely acid habitats, but also in moderate environments including ocean, lake and soil, which implies that archaea may contribute greatly to various ecosystems. By targeting the 16S rRNA gene with real-time PCR approaches, this paper studied the abundance of archaea, crenarchaea and bacteria from two agricultural soil profiles and two long-term fertilization stations Qiyang (QY) and Fengqiu (FQ). The 16S rRNA gene copy number of crenarchaea was 1-2 orders of magnitude lower than that of archaea, and the order of these three groups was crenarchaea < archaea < bacteria. The ratios of both archaea and crenarchaea to bacteria increased with soil depth. The abundance of archaea and crenarchaea had significantly different responses to different fertilization treatments. In QY station, the copy numbers of archaeal and bacterial 16S rRNA gene had significant positive correlations with soil pH (r = 0.850, P < 0.01 and r = 0.676, P < 0.05, respectively); in FQ station, all the 16S rRNA gene copy numbers of archaea, crenarchaea and bacteria had no significant correlations with soil pH, but significantly correlated with soil organic matter (r = 0.783, P < 0.05; r = 0. 827, P < 0.05; r = 0.767, P < 0.05, respectively). To understand the distribution of archaea and crenarchaea in agricultural soil could provide important information to evaluate their ecological functions in soil ecosystem and element cycling.

Purpose: Experiments were conducted to examine the effects of mercury (Hg) on soil nitrification activities and the microbial communities of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA)., Methods: The soil samples spiked with different Hg concentrations were incubated for a period of 1, 2, 4, and 8 weeks in triplicate and the potential nitrification rate (PNR) of the samples was determined. The abundance of AOB and AOA was measured after an 8-week incubation by real-time polymerase chain reaction (PCR) assay of the amoA genes, while the community compositions by cloning and sequencing approaches., Results: The soil PNR differed with different incubation periods. It tended to decrease with increasing soil Hg concentrations at week 1, basing on which the half-maximal effective concentration (EC50) was 1.59 mg kg(-1). There was no significant difference in the abundance of AOB or AOA among the treatments. The AOB community was dominated by Nitrosospira-like sequences and more than 70% of the obtained clones were affiliated with the cluster 3a.2. The percentage of cluster 3a.1 in AOB community appeared to a consistent trend of decreasing with ascending soil Hg concentrations. While all the AOA sequences in the clone libraries were grouped into cluster S (soil and sediment origin)., Conclusions: This study revealed that Hg could inhibit soil potential nitrification and the extent varied with incubation periods. Soil Hg pollution changed the composition of soil AOB to some extent. These findings will be helpful to recognize the effects of Hg on the activity and community composition of soil ammonia oxidizers.

To determine the abundance and distribution of bacterial and archaeal ammonia oxidizers in alpine and permafrost soils, 12 soils at altitudes of 4000-6550 m above sea level (m a.s.l.) were collected from the northern slope of the Mount Everest (Tibetan Plateau), where the permanent snow line is at 5800-6000 m a.s.l. Communities were characterized by real-time PCR and clone sequencing by targeting on amoA genes, which putatively encode ammonia monooxygenase subunit A. Archaeal amoA abundance was greater than bacterial amoA abundance in lower altitude soils (or=5700 m a.s.l.). Both archaeal and bacterial amoA abundance decreased abruptly in higher altitude soils. Communities shifted from a Nitrosospira amoA cluster 3a-dominated ammonia-oxidizing bacteria community in lower altitude soils to communities dominated by a newly designated Nitrosospira ME and cluster 2-related groups and Nitrosomonas cluster 6 in higher altitude soils. All archaeal amoA sequences fell within soil and sediment clusters, and the proportions of the major archaeal amoA clusters changed between the lower altitude and the higher altitude soils. These findings imply that the shift in the relative abundance and community structure of archaeal and bacterial ammonia oxidizers may result from selection of organisms adapted to altitude-dependent environmental factors in elevated soils.

Manganese (Mn) oxides are common minerals in natural environments that may play an important role in the biogeochemical cycles of heavy metals. Increasing evidences have shown that Mn (II) oxidation is a microbially-mediated process, and the Mn oxidizing microorganisms are thus recognized as the major drivers of the global Mn cycle. The major pathway for bacterial Mn (II) oxidation is catalysed by a multicopper oxidizing enzyme family. The primary Mn (IV) biooxides are phyllomanganate-like minerals most similar to delta-MnO2 or acid birnessite. Manganese oxides are known to have high sorption capacities for a wide variety of metal ions and considered to be the important environmental oxidant to many metal ions. This paper reviewed the mechanisms of biogenic manganese oxides formation and their reactions with heavy metal ions in environment.

The abundance and composition of soil ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) communities under different long-term (17 years) fertilization practices were investigated using real-time polymerase chain reaction and denaturing gradient gel electrophoresis (DGGE). A sandy loam with pH (H(2)O) ranging from 8.3 to 8.7 was sampled in years 2006 and 2007, including seven fertilization treatments of control without fertilizers (CK), those with combinations of fertilizer nitrogen (N), phosphorus (P) and potassium (K): NP, NK, PK and NPK, half chemical fertilizers NPK plus half organic manure (1/2OMN) and organic manure (OM). The highest bacterial amoA gene copy numbers were found in those treatments receiving N fertilizer. The archaeal amoA gene copy numbers ranging from 1.54 x 10(7) to 4.25 x 10(7) per gram of dry soil were significantly higher than those of bacterial amoA genes, ranging from 1.24 x 10(5) to 2.79 x 10(6) per gram of dry soil, which indicated a potential role of AOA in nitrification. Ammonia-oxidizing bacteria abundance had significant correlations with soil pH and potential nitrification rates. Denaturing gradient gel electrophoresis patterns revealed that the fertilization resulted in an obvious change of the AOB community, while no significant change of the AOA community was observed among different treatments. Phylogenetic analysis showed a dominance of Nitrosospira-like sequences, while three bands were affiliated with the Nitrosomonas genus. All AOA sequences fell within cluster S (soil origin) and cluster M (marine and sediment origin). These results suggest that long-term fertilization had a significant impact on AOB abundance and composition, while minimal on AOA in the alkaline soil.

Contemporary environmental disturbances and historical contingencies are considered to be major factors driving current differences in microbial diversity. However, little was known about their relative importance. This study combines culture-independent molecular techniques and advanced statistical analyses to examine quantitatively the relative importance of contemporary disturbances and historical contingencies in influencing large-scale soil bacterial diversity using a large set of manipulated field-based molecular data (212 samples). Contemporary disturbances were represented by applications of different fertilizers N, P, K and organic manure (OM) and historical contingencies by distinct geographic sampling locations and soil profiles. Multivariate regression tree (MRT) analysis showed that diversity estimates were mainly distinguished by sampling locations, which explained 40.8% of the variation in bacterial diversity, followed by soil profiles (19.5%), sampling time (13.1%), OM (3.7%) and P (1.8%). Aggregated boosted tree (ABT) analysis showed that the relative importance of different categorical factors on soil bacterial diversity variation was ranked as sampling locations, soil profiles, sampling time, OM and P. Both MRT and ABT analyses showed that historical contingencies were the dominant factor driving variation in bacterial diversity across a regional scale (about 1000 km), whereas some contemporary disturbances also caused variation in bacterial diversity at a local scale. This study demonstrated that past events and contemporary disturbances had similar influence on soil bacterial diversity to that documented for macroorganisms, indicating that there might be some common aspects of biogeography to all organisms.

The abundance and composition of soil ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) were investigated by using quantitative real-time polymerase chain reaction, cloning and sequencing approaches based on amoA genes. The soil, classified as agri-udic ferrosols with pH (H(2)O) ranging from 3.7 to 6.0, was sampled in summer and winter from long-term field experimental plots which had received 16 years continuous fertilization treatments, including fallow (CK0), control without fertilizers (CK) and those with combinations of fertilizer nitrogen (N), phosphorus (P) and potassium (K): N, NP, NK, PK, NPK and NPK plus organic manure (OM). Population sizes of AOB and AOA changed greatly in response to the different fertilization treatments. The NPK + OM treatment had the highest copy numbers of AOB and AOA amoA genes among the treatments that received mineral fertilizers, whereas the lowest copy numbers were recorded in the N treatment. Ammonia-oxidizing archaea were more abundant than AOB in all the corresponding treatments, with AOA to AOB ratios ranging from 1.02 to 12.36. Significant positive correlations were observed among the population sizes of AOB and AOA, soil pH and potential nitrification rates, indicating that both AOB and AOA played an important role in ammonia oxidation in the soil. Phylogenetic analyses of the amoA gene fragments showed that all AOB sequences from different treatments were affiliated with Nitrosospira or Nitrosospira-like species and grouped into cluster 3, and little difference in AOB community composition was recorded among different treatments. All AOA sequences fell within cluster S (soil origin) and cluster M (marine and sediment origin). Cluster M dominated exclusively in the N, NP, NK and PK treatments, indicating a pronounced difference in the community composition of AOA in response to the long-term fertilization treatments. These findings could be fundamental to improve our understanding of the importance of both AOB and AOA in the cycling of nitrogen and other nutrients in terrestrial ecosystems.

Most current microbial studies in paddy soils have focused on the top (0–20 cm) layer where rice roots are concentrated. To better understand the vertical distribution of microorganisms in paddy soils, we investigated the abundances, diversities and community compositions of archaea, bacteria and fungi in six geographically and climatically distinct paddy soil profiles from 0–80‐cm depth. Although microbial abundances and operational taxonomic unit (OTU) diversities largely decreased with soil depth, only the community composition of archaea (not bacteria or fungi) was associated with soil depth, echoing that only one archaeal OTU, but no bacterial or fungal OTUs, differed significantly in relative abundance between depth intervals. Mean annual temperature, precipitation and soil iron and manganese concentrations were significantly correlated with the ordinations of microbial communities for all three domains. Besides these common environmental factors, bacterial and archaeal community structures were also influenced by soil chloride and sulphate concentrations, whereas the concentrations of organic matter and total nitrogen were important explanatory factors for the variation in fungal community composition. Further analyses on putative bacterial functions showed significant differences between sampling sites rather than depth intervals, and suggested that bacterial OTUs that significantly varied in relative abundance across sampling sites might be functionally related to organic matter decomposition, sulphur oxidation and reduction, as well as nitrate reduction. Altogether, in the studied paddy soil profiles, the community composition and putative functions of bacteria were largely the same between different vertical layers, each with a thickness of 20 cm. This study suggests that the community compositions of archaea, bacteria and fungi are mainly driven by different soil chemical properties rather than soil depth, which could be linked to the ecological traits of the three microbial domains. Highlights: Communities of archaea, bacteria and fungi were investigated in six paddy soil profiles.Soil depth was only correlated with archaeal community structureEnvironmental factors influenced community composition differently for different domains.Bacterial OTUs contributing to variation in community composition among sites were functionally linked to C, N and S cycling. [ABSTRACT FROM AUTHOR]

Abstract: Flooded rice paddy soils represent a typical anaerobic freshwater habitat of microorganisms. The abundance and community structure of sulfate reducing prokaryotes (SRP) were investigated in order to understand their response to different fertilization practices in rice paddy, including control without fertilizers (CT) and arrangements of different chemical fertilizers of nitrogen (N), phosphorus (P) and potassium (K): N, NP, NK and NPK. The abundance of total bacteria and sulfate reducing prokaryotes of the rice paddy in summer and in winter were quantified by real-time PCR assays based on the 16S rRNA gene and the dissimilatory (bi)sulfite reductase gene (dsrAB) β-subunit. No significant differences in the bacterial and SRP abundance were observed among different fertilization treatments in both winter and summer. The mean copy numbers of bacteria was 7.26×109 copies g−1 dry soil in winter and 1.27×1010 copies g−1 dry soil in summer. The average dsrAB gene copy numbers of the SRP was 5.08×108 copies g−1 dry soil in winter and 5.92×108 copies g−1 dry soil in summer. The dsrAB gene clone libraries of the five fertilization treatments were constructed and their RFLP analysis yielded 22–25 restriction patterns, suggesting a high degree of dsrAB sequence diversity in different fertilization treatments. There was no significant change in the soil SRP community structure among the different fertilization regimes. More than half of the sequences were affiliated with novel branching clusters which were uncultured SRP. Clostridia and Deltaproteobacteria were also found with a high proportion in the clone libraries, while Desulfovibrionaceae was absent. High proportion of novel uncultured SRP implies that they may play important roles in paddy soils and deserve further studies. [Copyright &y& Elsevier]