Biodegradable film mulching increases soil microbial network complexity and decreases nitrogen-cycling gene abundance.

Biodegradable plastic films have emerged as a substitute for conventional plastic films. Nevertheless, responses of plant-associated microbiomes to the application of biodegradable film mulching at field scale have received little attention. A field experiment was conducted to assess the influence of different film mulching treatments on various microbial attributes and nitrogen (N) cycling functional genes in bulk and rhizosphere soils. Biodegradable film mulching raised the bacterial Shannon index in bulk soils but not in rhizosphere soils. Biodegradable film mulching has led to an increase in the complexity and connectivity of microbial networks, as well as an enhancement in the positive association among microorganisms owing to raised soil nutrients and increased crop biomass. In biodegradable film-treated soils, both bacterial and fungal communities were primarily influenced by stochastic processes associated with dispersal limitation. Moreover, conventional plastic film mulching increased denitrification, anammox, N fixation, and dissimilatory nitrate-reduction (DNRA) gene abundance in bulk soils. In rhizosphere soils, biodegradable film mulching reduced nitrification, denitrification, anammox, N fixation, and DNRA gene abundance. Furthermore, keystone genera (e.g., Nitrosospira, Truepera, Adhaeribacter, Opitutus, and Fusarium) were affected by edaphic variables, contributing to decreased N-cycling gene abundance in biodegradable film-treated soils. Collectively, biodegradable film mulching transformed soil microbiome assembly and functional adaptation, and soil nutrient availability and plant biomass were the critical factors influencing the microbial community. These findings present a novel perspective on the diverse impacts of biodegradable and conventional film mulching on soil microbiome and N-cycling processes.

Enhancing soil health and nutrient cycling through soil amendments: Improving the synergy of bacteria and fungi.

The synergy between bacteria and fungi is a key determinant of soil health and have a positive effect on plant development under drought conditions, with the potentially enhancing the sustainability of amending soil with natural materials. However, identifying how soil amendments influence plant growth is often difficult due to the complexity of microorganisms and their links with different soil amendment types and environmental factors. To address this, we conducted a field experiment to examine the impact of soil amendments (biochar, Bacillus mucilaginosus, Bacillus subtilis and super absorbent polymer) on plant growth. We also assessed variations in microbial community, links between fungi and bacteria, and soil available nutrients, while exploring how the synergistic effects between fungus and bacteria influenced the response of soil amendments to plant growth. This study revealed that soil amendments reduced soil bacterial diversity but increased the proportion of the family Enterobacteriaceae, Nitrosomonadaceae, and also increased soil fungal diversity and the proportion of the sum of the family Lasiosphaeriaceae, Chaetomiaceae, Pleosporaceae. Changes in soil microbial communities lead to increase the complexity of microbial co-occurrence networks. Furthermore, this heightened network complexity enhanced the synergy of soil bacteria and fungi, supporting bacterial functions related to soil nutrient cycling, such as metabolic functions and genetic, environmental, and cellular processes. Hence, the BC and BS had 3.0-fold and 0.5-fold greater root length densities than CK and apple tree shoot growth were increased by 62.14 %,50.53 % relative to CK, respectively. In sum, our results suggest that the synergistic effect of bacteria and fungi impacted apple tree growth indirectly by modulating soil nutrient cycling. These findings offer a new strategy for enhancing the quality of arable land in arid and semi-arid regions.

Host genotype-specific rhizosphere fungus enhances drought resistance in wheat.

BACKGROUND: The severity and frequency of drought are expected to increase substantially in the coming century and dramatically reduce crop yields. Manipulation of rhizosphere microbiomes is an emerging strategy for mitigating drought stress in agroecosystems. However, little is known about the mechanisms underlying how drought-resistant plant recruitment of specific rhizosphere fungi enhances drought adaptation of drought-sensitive wheats. Here, we investigated microbial community assembly features and functional profiles of rhizosphere microbiomes related to drought-resistant and drought-sensitive wheats by amplicon and shotgun metagenome sequencing techniques. We then established evident linkages between root morphology traits and putative keystone taxa based on microbial inoculation experiments. Furthermore, root RNA sequencing and RT-qPCR were employed to explore the mechanisms how rhizosphere microbes modify plant response traits to drought stresses. RESULTS: Our results indicated that host plant signature, plant niche compartment, and planting site jointly contribute to the variation of soil microbiome assembly and functional adaptation, with a relatively greater effect of host plant signature observed for the rhizosphere fungi community. Importantly, drought-resistant wheat (Yunhan 618) possessed more diverse bacterial and fungal taxa than that of the drought-sensitive wheat (Chinese Spring), particularly for specific fungal species. In terms of microbial interkingdom association networks, the drought-resistant variety possessed more complex microbial networks. Metagenomics analyses further suggested that the enriched rhizosphere microbiomes belonging to the drought-resistant cultivar had a higher investment in energy metabolism, particularly in carbon cycling, that shaped their distinctive drought tolerance via the mediation of drought-induced feedback functional pathways. Furthermore, we observed that host plant signature drives the differentiation in the ecological role of the cultivable fungal species Mortierella alpine (M. alpina) and Epicoccum nigrum (E. nigrum). The successful colonization of M. alpina on the root surface enhanced the resistance of wheats in response to drought stresses via activation of drought-responsive genes (e.g., CIPK9 and PP2C30). Notably, we found that lateral roots and root hairs were significantly suppressed by co-colonization of a drought-enriched fungus (M. alpina) and a drought-depleted fungus (E. nigrum). CONCLUSIONS: Collectively, our findings revealed host genotypes profoundly influence rhizosphere microbiome assembly and functional adaptation, as well as it provides evidence that drought-resistant plant recruitment of specific rhizosphere fungi enhances drought tolerance of drought-sensitive wheats. These findings significantly underpin our understanding of the complex feedbacks between plants and microbes during drought, and lay a foundation for steering "beneficial keystone biome" to develop more resilient and productive crops under climate change. Video Abstract.

Fertilizing-induced alterations of microbial functional profiles in soil nitrogen cycling closely associate with crop yield.

Fertilization and rhizosphere selection are key regulators for soil nitrogen (N) cycling and microbiome. Thus, clarifying how the overall N cycling processes and soil microbiome respond to these factors is a prerequisite for understanding the consequences of high inputs of fertilizers, enhancing crop yields, and formulating reasonable nitrogen management strategies under agricultural intensification scenarios. To do this, we applied shotgun metagenomics sequencing to reconstruct N cycling pathways on the basis of abundance and distribution of related gene families, as well as explored the microbial diversity and interaction via high throughput sequencing based on a two-decade fertilization experiment in Loess Plateau of China semiarid area. We found that bacteria and fungi respond divergent to fertilization regimes and rhizosphere selection, in terms of community diversity, niche breadth, and microbial co-occurrence networks. Moreover, organic fertilization decreased the complexity of bacterial networks but increased the complexity and stability of fungal networks. Most importantly, rhizosphere selection exerted more strongly influences on the soil overall nitrogen cycling than the application of fertilizers, accompanied by the increase in the abundance of nifH, NIT-6, and narI genes and the decrease in the abundance of amoC, norC, and gdhA genes in the rhizosphere soil. Furthermore, keystone families screening from soil microbiome (e.g., Sphingomonadaceae, Sporichthyaceae, and Mortierellaceae), which were affected by the edaphic variables, contributed greatly to crop yield. Collectively, our findings emphasize the pivotal roles of rhizosphere selection interacting with fertilization regimes in sustaining soil nitrogen cycling processes in response to decades-long fertilization, as well as the potential importance of keystone taxa in maintaining crop yield. These findings significantly facilitate our understanding of nitrogen cycling in diverse agricultural soils and lay a foundation for manipulating specific microorganisms to regulate N cycling and promote agroecosystem sustainability.

Plant domestication shapes rhizosphere microbiome assembly and metabolic functions.

BACKGROUND: The rhizosphere microbiome, which is shaped by host genotypes, root exudates, and plant domestication, is crucial for sustaining agricultural plant growth. Despite its importance, how plant domestication builds up specific rhizosphere microbiomes and metabolic functions, as well as the importance of these affected rhizobiomes and relevant root exudates in maintaining plant growth, is not well understood. Here, we firstly investigated the rhizosphere bacterial and fungal communities of domestication and wild accessions of tetraploid wheat using amplicon sequencing (16S and ITS) after 9 years of domestication process at the main production sites in China. We then explored the ecological roles of root exudation in shaping rhizosphere microbiome functions by integrating metagenomics and metabolic genomics approaches. Furthermore, we established evident linkages between root morphology traits and keystone taxa based on microbial culture and plant inoculation experiments. RESULTS: Our results suggested that plant rhizosphere microbiomes were co-shaped by both host genotypes and domestication status. The wheat genomes contributed more variation in the microbial diversity and composition of rhizosphere bacterial communities than fungal communities, whereas plant domestication status exerted much stronger influences on the fungal communities. In terms of microbial interkingdom association networks, domestication destabilized microbial network and depleted the abundance of keystone fungal taxa. Moreover, we found that domestication shifted the rhizosphere microbiome from slow growing and fungi dominated to fast growing and bacteria dominated, thereby resulting in a shift from fungi-dominated membership with enrichment of carbon fixation genes to bacteria-dominated membership with enrichment of carbon degradation genes. Metagenomics analyses further indicated that wild cultivars of wheat possess higher microbial function diversity than domesticated cultivars. Notably, we found that wild cultivar is able to harness rhizosphere microorganism carrying N transformation (i.e., nitrification, denitrification) and P mineralization pathway, whereas rhizobiomes carrying inorganic N fixation, organic N ammonification, and inorganic P solubilization genes are recruited by the releasing of root exudates from domesticated wheat. More importantly, our metabolite-wide association study indicated that the contrasting functional roles of root exudates and the harnessed keystone microbial taxa with different nutrient acquisition strategies jointly determined the aboveground plant phenotypes. Furthermore, we observed that although domesticated and wild wheats recruited distinct microbial taxa and relevant functions, domestication-induced recruitment of keystone taxa led to a consistent growth regulation of root regardless of wheat domestication status. CONCLUSIONS: Our results indicate that plant domestication profoundly influences rhizosphere microbiome assembly and metabolic functions and provide evidence that host plants are able to harness a differentiated ecological role of root-associated keystone microbiomes through the release of root exudates to sustain belowground multi-nutrient cycles and plant growth. These findings provide valuable insights into the mechanisms underlying plant-microbiome interactions and how to harness the rhizosphere microbiome for crop improvement in sustainable agriculture. Video Abstract.

Weak environmental adaptation of rare phylotypes sustaining soil multi-element cycles in response to decades-long fertilization.

Deciphering the ecological role of soil communities in the maintenance of multiple ecosystem functions is pivotal for the conservation and sustainability of soil biodiversity. However, few studies have investigated niche differentiation of abundant and rare microbiota, as well as their contributions to multiple soil elemental cycles, particularly in agroecosystems that have received decades of intense fertilization. Here, we characterized the environmental thresholds and phylogenetic signals for the environmental adaptation of both abundant and rare microbial subcommunities via amplicon sequencing and metagenomic sequencing and explored their importance in sustaining soil multiple nutrient cycling in agricultural fields that were fertilized for two decades. The results showed that rare taxa exhibited narrower niche breadths and weaker phylogenetic signals than abundant species. The assembly of abundant subcommunity was shaped predominantly by dispersal limitation (explained 71.1 % of the variation in bacteria) and undominated processes (explained 75 % of the variation in fungi), whereas the assembly of rare subcommunity was dominated by homogeneous selection process (explained 100 % of the variation in bacteria and 60 % of the variation in fungi). Soil ammonia nitrogen was the leading factor mediating the balance between stochastic and deterministic processes in both abundant (R2 = 0.15, P < 0.001) and rare (R2 = 0.08, P < 0.001) bacterial communities. Notably, the rare biosphere largely contributed to key soil processes such as carbon (R2bacteria = 0.03, P < 0.05; R2fungi = 0.05, P < 0.05) and nitrogen (R2bacteria = 0.03, P < 0.05; R2fungi = 0.17, P < 0.001) cycling. Collectively, these findings facilitate our understanding of the maintenance of rhizosphere bacterial and fungal diversity in response to agricultural fertilization and highlight the key role of rare taxa in sustaining agricultural ecosystem functions.

Fertilization regimes affect crop yields through changes of diazotrophic community and gene abundance in soil aggregation.

Soil aggregates are extremely vulnerable to agricultural intensification and are important drivers of soil health, microbial diversity, and biogeochemical cycling. Despite its importance, there is a dearth of studies revealing how fertilization regimes influence diazotrophic community behind soil aggregates, as well as the potential consequences for crop yields. To do this, a two-decade fertilization of wheat-maize intercropping field experiment was conducted in Loess Plateau of China semiarid area under three treatments: no fertilizer, chemical and organic fertilizer. Moreover, we categorized soil aggregates as large macroaggregates (>2 mm), medium macroaggregates (1-2 mm), small macroaggregates (0.25-1 mm), microaggregates (< 0.25 mm) and rhizosphere soils aggregates. We found that soil aggregates exerted a much more influence on the nifH gene abundance than fertilization practices. Particularly, nifH gene abundance has been promoted with increasing the size of soil aggregates fraction without blank soil in the organic fertilization while its abundance presented contrast patterns in the chemical fertilization. Bipartite association networks indicated that different soil aggregates shaped niche differentiation of diazotrophic community behind fertilization regimes. Additionally, we found that organic fertilization strengthens the robustness of diazotrophic communities as well as increases the complexity of microbial networks by harboring keystone taxa. Mantel test results suggested that specific soil factors exerted more selective power on diazotrophic community and nifH gene abundance in the chemical fertilization. Furthermore, ß-diversity and nifH gene abundance of diazotrophic communities in the soil microaggregates jointly determine the crop yields. Collectively, our findings emphasize the key role of functional community diversity in sustaining soil cycling process and crop yields under long-term fertilization, and facilitate our understanding of the mechanisms underlying diazotrophic community in response to agricultural intensification, which could pave the way to sustainable agriculture through manipulating the functional taxa.

Soil pH determines arsenic-related functional gene and bacterial diversity in natural forests on the Taibai Mountain.

Arsenic-related functional genes are ubiquitous in microbes, and their distribution and abundance are influenced by edaphic factors. In arsenic-contaminated soils, soil arsenic content and pH determine the distribution of arsenic metabolizing microorganisms. In the uncontaminated natural ecosystems, however, it remains understudied for the key variable factor in determining the variation of bacterial assembly and mediating the arsenic biogeographical cycles. Here, we selected natural forest soils from southern and northern slopes along the altitudinal gradient of Taibai Mountain, China. The arsenic-related functional genes and soil bacterial community was examined using GeoChip 5.0 and high-throughput sequencing of 16S rRNA genes, respectively. It was found that arsenic-related functional genes were ubiquitous in tested forest soils. The gene arsB has the highest relative abundance, followed by arsC, aoxB, arrA, arsM, and arxA. The arsenic-related functional genes distribution on two slopes were decoupled from their corresponding bacterial community. Though there are higher abundance of bacterial communities on the northern slope than that on the southern slope, for arsenic-related functional genes, the abundance has the contrary trend which showing the more arsenic-related functional genes on the southern slope. In the top ten phyla, Proteobacteria and Actinobacteria were dominant phyla which affected the abundance of arsenic-related functional genes. Redundancy analysis and variance partitioning analysis indicated that soil pH, organic matter and altitude jointly determined the arsenic-related functional genes diversity in the two slopes of Taibai Mountain, and soil pH was a key factor. This indicates that the lower pH may shape more microbes with arsenic metabolic capacity. These findings suggested that soil pH plays a significant role in regulating the distribution of arsenic-related functional microorganisms, even for a forest ecosystem with an altitudinal gradient, and remind us the importance of pH in microbe mediated arsenic transformation.

Fertilizing-induced changes in the nitrifying microbiota associated with soil nitrification and crop yield.

Ammonia oxidizing archaea (AOA) and bacteria (AOB), nitrite-oxidizing bacteria (NOB), and comammox Nitrospira (CMX) play pivotal roles in global nitrogen-cycling network. Despite its importance, the driving forces for niche specialization of these nitrifiers, as well as their relative contributions to nitrification and crop yield have not been fully understood. Here, we investigated the niche specialization and environmental prevalence of nitrifying communities, and their importance for the nitrification rate and crop yield across a gradient of nitrogen inputs in a two-decade old field experiment. The results of 15N-tracer and quantitative PCR revealed that AOB and NOB jointly determined the gross nitrification rates across mineral fertilizer treatments, whereas AOA and AOB contributed more than other nitrifiers to nitrification under with organic fertilizer amendments. Linear regression model revealed that crop yield could be linked with AOB and NOB under inorganic farming but closely associated with CMX under organic management. Amplicon sequencing of these functional genes further demonstrated that mineral and organic fertilizers have distinct influences on the ß-diversity and niche breadth of these nitrifying communities, indicating that fertilization triggered niche specialization of nitrifying guilds in agricultural soils. Notably, organic fertilization enhanced the network complexity of these nitrifiers by harboring keystone taxa. Random forest analysis provide robustly evidence for the hypothesis that abundance of functional genes contributed more than a- and ß-diversity of these nitrifiers for driving nitrification rates and crop yields. Collectively, these findings provide the empirical evidence for the environmental adaptation and niche specialization of nitrifying communities, and their contributions in nitrification and crop yield when confronted with long-term nitrogen inputs.

Rare prokaryotic sub-communities dominate the complexity of ecological networks and soil multinutrient cycling during long-term secondary succession in China's Loess Plateau.

Unraveling the succession of microbial communities is a core ecological research topic. Yet few studies have focused on how long-term secondary succession affects the functional profiles and ecological processes of abundant and rare microbial subcommunities. Here, we used amplicon sequencing and GeoChip analysis to explore the ecological functions of abundant and rare biospheres and their correlation with soil multinutrient cycling. Samples for this study were collected from a well-established secondary succession chronosequence that spans >30 years of dryland ecosystem development on the Loess Plateau of China. Although both abundant and rare subcommunities shifted with succession, the changing of beta-diversity of the microbial communities was primarily driven by species replacement of the rare biosphere. Phylogenetic changes of abundant and rare taxa were associated with their functional traits, which dominated the diversity-related selection along all succession ages. Neutral theory analysis indicated that the assemblage of abundant taxa over all successional ages was regulated by dispersal homogenizing and ecological drift. The null model revealed that homogeneous and variable selection were the dominant assembly processes for rare subcommunities compared with abundant species. pH and nitrogen content were the paramount drivers determining the assembly of microbial communities and functional genes, consistent with the importance of environmental filtering. Furthermore, the rare biosphere had a paramount role in the entire ecological network and was the major driver for most soil processes such as C, N, and S cycling. Nonetheless, a significant portion of soil P cycling was regulated by abundant taxa. Collectively, our study provides insight into the mechanisms underlying microbial community assembly and soil microbe-driven functional changes in biogeochemical processes during secondary succession.

Inter-phylum negative interactions affect soil bacterial community dynamics and functions during soybean development under long-term nitrogen fertilization.

Understanding interspecies interactions is essential to predict the response of microbial communities to exogenous perturbation. Herein, rhizospheric and bulk soils were collected from five developmental stages of soybean, which grew in soils receiving 16-year nitrogen inputs. Bacterial communities and functional profiles were examined using high-throughput sequencing and quantitative PCR, respectively. The objective of this study was to identify the key bacterial interactions that influenced community dynamics and functions. We found that the stages of soybean development outcompeted nitrogen fertilization management in shaping bacterial community structure, while fertilization treatments significantly shaped the abundance distribution of nitrogen functional genes. Temporal variations in bacterial abundances increased in bulk soils, especially at the stage of soybean branching, which helps to infer underlying negative interspecies interactions. Members of Cyanobacteria and Actinobacteria actively engaged in inter-phylum negative interactions in bulk soils and soybean rhizosphere, respectively. Furthermore, the negative interactions between nitrogen-fixing functional groups and the reduction of nifH gene abundance were coupled during soybean development, which may help to explain the linkages between population dynamics and functions. Overall, these findings highlight the importance of inter-phylum negative interactions in shaping the correlation patterns of bacterial communities and in determining soil functional potential.

Keystone taxa regulate microbial assemblage patterns and functional traits of different microbial aggregates in simultaneous anammox and denitrification (SAD) systems.

Understanding the impacts of the ecological patterns and niche-based selection on microbial community assembly and nitrogen-cycling network is crucial for achieving energy-neutral wastewater treatment. However, little is known about the niche differentiation and microbial nitrogen-cycling traits of keystone taxa in flocs and granules in anammox-based systems. Herein, the aspects of community assemblage patterns, metabolic functions and nitrogen transformation pathways were explored. The findings discovered that the treatment performance and bacterial community assembly were regulated by core taxa and flocs and granules communities harbored core taxa based on their functional traits. Both niche differentiation and environmental filtering have profound influences on functional bacteria. Furthermore, a combined analysis showed that nitrogen removal in flocs and granules was regulated by different nitrogen transformation pathways. These results suggest that core taxa are the key drivers for the microbial nitrogen-cycling network and improve the understanding of cross-feeding and metabolic pathways between anammox and nitrogen-cycling-related microorganisms.

rDNA- and rRNA-derived communities present divergent assemblage patterns and functional traits throughout full-scale landfill leachate treatment process trains.

Understanding the influences of microbial interactions and niche heterogeneities on microbial communities and functional traits is critical for determining its engineering and ecological significance. However, little is known about microbial community assemblage and functional gene expression throughout full-scale landfill leachate treatment plants. Here, we applied a combination of 16S rRNA and rDNA amplicon sequencing, shotgun metagenomic, and qPCR approaches to unveil the ecological associations between distinct communities, functional gene expression and nitrogen cycling processes. By comparing the rDNA and rRNA-derived communities, the rRNA/rDNA ratios suggested that 57.2% of rare taxa were active, and their abundance decreased as increasing of potential activities. In particular, rDNA- and rRNA-based communities exhibited divergent assemblage patterns, and stronger intra-associations among core taxa in the rRNA-based communities than in rDNA-based communities. Furthermore, results regarding both bacterial assemblage and functional traits indicated that the habitat filtering and niche differentiation (treatment units) exerted selection on microbial communities based on functional traits, particular for key ecological functions related to nitrogen cycling. Collectively, our findings provide insights into structure-function associations at the local level and shed light on ecological rules guiding rDNA- and rRNA-based community assembly in landfill leachate treatment systems.

Abundant and rare microbial sub-communities in anammox granules present contrasting assemblage patterns and metabolic functions in response to inorganic carbon stresses.

Nitrogen-transforming microorganisms play pivotal roles for the microbial nitrogen-cycling network in the anammox granular system. However, little is known about the effects of inorganic carbon (IC) stresses on the assemblage patterns and functional profiles of abundant and rare taxa. Herein, the community assemblage and functional traits of abundant and rare sub-communities were investigated. Results revealed that insufficient IC had adverse influences on the process performance, while anammox activity could be recovered by IC addition. Co-occurrence network analysis indicated that abundant and rare sub-communities present divergent co-occurrence patterns. Additionally, environmental filtering had different influences on the ecological adaptability of bacterial sub-communities. Furthermore, qPCR results illustrated that NH4+-N and NO2--N consumption were regulated by abundant sub-community, while their accumulation was mediated by rare sub-community. Collectively, these findings suggest that abundant and rare sub-communities present contrasting assemblage patterns and metabolic pathways, and functional profiles dominated selection of bacterial sub-communities under IC stresses.

Divergent assemblage patterns of abundant and rare microbial sub-communities in response to inorganic carbon stresses in a simultaneous anammox and denitrification (SAD) system.

Inorganic carbon has profound influence on anammox system and distinct microbial communities play pivotal roles in nitrogen removal, yet little is known about the ecological patterns of abundant and rare sub-communities in response to inorganic carbon stresses in simultaneous anammox and denitrification systems. Here the aspects of community ecology of abundant and rare taxa under abiotic constraints were explored. Results showed that different IC/NH4+-N ratios have significant influences on NH4+-N and TN removal. Co-occurrence networks revealed that abundant and rare taxa present contrasting assemblage patterns and ecological strategies. Spearman's correlation indicated that environmental filtering had discrepancy influences on these two bacterial sub-communities. Moreover, rare taxa were the key regulators for NH4+-N accumulation and NO2--N consumption. qPCR results indicated that nitrogen removal was mediated by multiple nitrogen transformation pathways. These findings collectively suggest that abundant and rare sub-communities have discrepant ecological patterns and provide insights into their structure-functional relationships.

Genome-Wide Identification and Expression Analysis of the HD-Zip Gene Family in Wheat (Triticum aestivum L.).

The homeodomain-leucine zipper (HD-Zip) gene family, as plant-specific transcription factors, plays an important role in plant development and growth as well as in the response to diverse stresses. Although HD-Zip genes have been extensively studied in many plants, they had not yet been studied in wheat, especially those involved in response to abiotic stresses. In this study, 46 wheat HD-Zip genes were identified using a genome-wide search method. Phylogenetic analysis classified these genes into four groups, numbered 4, 5, 17 and 20 respectively. In total, only three genes with A, B and D homoeologous copies were identified. Furthermore, the gene interaction networks found that the TaHDZ genes played a critical role in the regulatory pathway of organ development and osmotic stress. Finally, the expression profiles of the wheat HD-Zips in different tissues and under various abiotic stresses were investigated using the available RNA sequencing (RNA-Seq) data and then validated by quantitative real-time polymerase chain reaction (qRT-PCR) to obtain the tissue-specific and stress-responsive candidates. This study systematically identifies the HD-Zip gene family in wheat at the genome-wide level, providing important candidates for further functional analysis and contributing to the better understanding of the molecular basis of development and stress tolerance in wheat.

Taxonomical and functional microbial community dynamics in an Anammox-ASBR system under different Fe (III) supplementation.

In the present study, we explored the metabolic versatility of anaerobic ammonium oxidation (anammox) bacteria in a variety of Fe (III) concentrations. Specifically, we investigated the impacts of Fe (III) on anammox growth rates, on nitrogen removal performance, and on microbial community dynamics. The results from our short-term experiments revealed that Fe (III) concentrations (0.04-0.10 mM) significantly promote the specific anammox growth rate from 0.1343 to 0.1709 d-1. In the long-term experiments, the Anammox-anaerobic sequencing batch reactor (ASBR) was operated over 120 days and achieved maximum NH4+-N, NO2--N, and TN efficiencies of 90.98 ± 0.35, 93.78 ± 0.29, and 83.66 ± 0.46 %, respectively. Pearson's correlation coefficients between anammox-(narG + napA), anammox-nrfA, and anammox-FeRB all exceeded r = 0.820 (p < 0.05), confirming an interaction and ecological association among the nitrogen and iron-cycling-related microbial communities. Illumina MiSeq sequencing indicated that Chloroflexi (34.39-39.31 %) was the most abundant phylum in an Anammox-ASBR system, followed by Planctomycetes (30.73-35.31 %), Proteobacteria (15.40-18.61 %), and Chlorobi (4.78-6.58 %). Furthermore, we found that higher Fe (III) supplementation (>0.06 mM) could result in the community succession of anammox species, in which Candidatus Brocadia and Candidatus Kuenenia were the dominant anammox bacteria species. Combined analyses indicated that the coupling of anammox, dissimilatory nitrogen reduction to ammonium, and iron reduction accounted for nitrogen loss in the Anammox-ASBR system. Overall, the knowledge gained in this study provides novel insights into the microbial community dynamics and metabolic potential of anammox bacteria under Fe (III) supplementation.

Metagenomic insights into the effects of volatile fatty acids on microbial community structures and functional genes in organotrophic anammox process.

To explore the metabolic versatility of "Candidatus Brocadia sinica" in the presence of VFAs, the impacts of VFAs on anammox activity and nitrogen removal were investigated in this study. Results found that low VFAs concentrations has no affect on anammox activity and the removal efficiencies of NH4(+)-N and NO2(-)-N. However, "Ca. Brocadia sinica" showed higher adaptability to some VFAs stresses. Furthermore, Illumina MiSeq pyrosequencing results indicated that the microbial community structures varied significantly and the phyla Chloroflexi, Proteobacteria, Bacteroidetes and Chlorobi were dominated. Finally, qPCR was performed to validate the growth of anammox bacteria and gain the quantitative insights into the correlation between nitrogen transformation rates and the key functional genes in the organotrophic anammox system. Combined analysis clearly demonstrated that the coupling of the anammox, denitrification and DNRA were the noteworthy pathway for the simultaneous removal of nitrogen and organic carbon.

Microbial structures and community functions of anaerobic sludge in six full-scale wastewater treatment plants as revealed by 454 high-throughput pyrosequencing.

The microbial communities and abundance in anaerobic sludge from 4 industrial and 2 municipal wastewater treatment plants were investigated using 454 pyrosequencing technology in this study. A total of 5482-8692 high-quality reads of 16S rRNA V3-V5 regions were obtained. Taxonomic analysis using QIIME and RDP classifier found that Proteobacteria, Bacteroidetes, Chloroflexi and Firmicutes were the most abundant phyla in these samples. Furthermore, real-time PCR was used to validate the absolute abundance of these 16S rRNAs and some functional genes, including total bacteria, anammox bacteria, NOB (Nitrobacter, Nitrospira), AOA amoA, AOB amoA, nosZ, nirS, nirK, narG, napA, nrfA, mcrA and dsrA. Multivariate linear regression analysis indicated that AOA might be mixotrophic. Finally, redundancy analysis was used to reveal the relationships between operation parameters and microbial communities. Results showed that the coexistence of anammox, denitrification and DNRA could be useful for the simultaneous removal of nitrogen and organic matter.