Bacterial Community Function Research Articles

Over two years study: Peanut biochar promoted potassium availability by mediating the relationship between bacterial community and soil properties

In acidic soil, potassium (K) deficiency is a main limiting factor that restricts the growth of fruit trees. Biochar has been used as a soil amendment to increase pH and nutrients. However, studies on the effect of biochar on the bacterial community and soil properties in potted experiments are limited. Therefore, we used peanut shell biochar to investigate the effect of biochar on the structure and function of bacterial communities by high-throughput sequencing, soil enzymes (urease, dehydrogenase, and extracellular enzymes), and gene function prediction in response to K deficiency in acidic soil. The results indicated that soil pH, enzyme activity, and available nutrients were improved by biochar. In particular, biochar still had a beneficial effect on improving soil and plant K levels after thirty months of application. In addition, biochar promoted the growth of K-dissolving bacteria and relative abundance of bacteria (p_actinomycetes, p_chloroflexi, p_proteobacteria, p_acidobacteriota, and p_firmicutes). Based on the above results, we assumed that biochar application can effectively improve soil K levels and bacterial functions. Such as: K-dissolving, soil organic matter decomposition and the conversion of nutrients. Our findings encourage and support the use of biochar as an amendment in acidic soil.

Primary carbon sources and self-induced metabolic landscapes shape community structure in soil bacterial hotspots

Direct observations of the complex and highly dynamic metabolic landscapes that affect the structure and functioning of bacterial communities in natural soil are limited by soil opacity and pore space complexity. In this study, we employ community metabolic network models to predict how the emerging bacterial community composition alters its structure and composition as a function of the primary carbon source in both well-mixed and spatially explicit systems. We provide systematic, experimental validation using a synthetic community comprised of four bacterial species grown on prescribed carbon sources and quantify their abundance using qPCR. Results suggest that community members may benefit from trophic interactions or suffer from increased competitive stress depending on the carbon source. The modeling is expanded to consider interactions in soil-like spatial context. Results show emergence of distinct bacterial community compositions as a function of primary carbon sources typical to soil hotspots (carbohydrates or organic acids). The ability to link genetic information with bacterial community trophic interactions in representative soil environments is a critical first step towards attaining predictability of soil ecological functioning.

Comparative transcriptomic and metagenomic analyses reveal key factors affecting the growth rate of Red Swamp Crayfish (Procambarus clarkii)

Even under highly-controlled growth conditions, sibling individuals of red swamp crayfish (Procambarus clarkii) frequently exhibit stunting. To elucidate the causes of stunting, we compared the hepatopancreas transcriptome and intestinal flora of sibling crayfish. Individual variations were investigated, and the association of gut bacterial community function with host transcriptome function was explored. A total of 60,637,958 single genes were assembled from 300,691,028 high-quality reads. When the expression patterns of crayfish hepatopancreas of various sizes were compared, 497 differentially expressed genes (P < 0.05) were discovered. KEGG database and GO functional annotation were conducted, revealing 32 enriched KEGG signaling pathways, with the most significant enrichment seen in genes associated with fatty acid production. We additionally found enrichment in other metabolism-related enzymes (AMS, Gls, and Lps) and immune-related enzymes (Lyz, SOD, and Ppo) when comparing rapidly growing individuals to slowly growing individuals. Furthermore, we discovered that Proteobacteria, Tenericutes, Actinomycetes, and Cyanobacteria bacteria were more prevalent in the microbiomes of rapidly growing individuals, implying that the crayfish microbiota is adapted to fast growth and may promote accelerated development by regulating the expression levels of metabolic genes. These results lay the foundation for future studies focused on the association between crayfish intestinal flora and growth rate.

Spatial and temporal changes in bacterial community structure in adjacent waters of Dagu River estuary of Jiaozhou Bay (China) revealed by high-throughput sequencing

Dagu River, the largest sea-entering river in Jiaozhou Bay, middle of Yellow Sea (China) which has a significant impact on the waters adjacent to the estuary In this study, the bacterial abundance and community of seawater in adjacent waters of Dagu River estuary were investigated over four seasons using flow cytometry and high-throughput sequencing techniques. The bacterial abundance showed significant seasonal differences and the average abundance was highest in summer, followed by autumn, and lowest in spring, while the horizontal distribution in winter showed a higher bacterial abundance in nearshore waters. Temperature, phytoplankton abundance and virus abundance were the main factors influencing bacterial abundance. In addition, the dominant taxa of the bacterial community were the same among different seasons, but the relative abundance varied seasonally and there was no significant difference in the bacterial community structure among different stations. Proteobacteria and Bacteroides were the core groups in all seasons. Additionally, temperature and salinity were the major drivers of bacterial community. Moreover, the predicted bacterial functions in investigated waters were mainly focused on carbon and sulfur cycles, and there were seasonal differences in bacterial community function, but the spatial difference was not significant. These results indicated that the bacterial community structure in the waters adjacent to the Dagu River estuary was shaped more by seasonal variation than by spatial variation and provide the basic data and further understanding of characteristics of bacterial community structure in the semi-enclosed shallow bay.

Spatiotemporal Dynamics of Bacterial Taxonomic and Functional Profiles in Estuarine Intertidal Soils of China Coastal Zone.

Bacteria play an important role in regulating carbon (C), nitrogen (N), and sulfur (S) in estuarine intertidal wetlands. To gain insights into the ecological and metabolic modes possessed by bacteria in estuarine intertidal wetlands, a total of 78 surface soil samples were collected from China's coastal intertidal wetlands to examine the spatial and seasonal variations of bacterial taxonomic composition, assembly processes, and ecological system functions through shotgun metagenomic and 16S rRNA gene sequencing. Obvious spatiotemporal dynamic patterns in the bacterial community structure were identified, with more pronounced seasonal rather than spatial variations. Dispersion limitation was observed to act as a critical factor affecting community assembly, explaining approximately half of the total variation in the bacterial community. Functional bacterial community structure exhibited a more significant latitudinal change than seasonal variability, highlighting that functional stability of the bacterial communities differed with their taxonomic variability. Identification of biogeochemically related links between C, N, and S cycles in the soils showed the adaptive routed metabolism of the bacterial communities and the strong interactions between coupled metabolic pathways. Our study broadens the insights into the taxonomic and functional profiles of bacteria in China's estuarine intertidal soils and helps us understand the effects exerted by environmental factors on the ecological health and microbial diversity of estuarine intertidal flats.

Effects of sediment physicochemical factors and heavy metals on the diversity, structure, and functions of bacterial and fungal communities from a eutrophic river

Urbanization has destroyed river ecosystems, leading to eutrophication. Heavy metals are frequently observed in urban rivers, and the joint effects of eutrophication and heavy metals on microbial communities, especially on fungal communities, have not been adequately explored. In this study, we explored the effect of sediment physicochemical factors and heavy metals on the microbial diversity, community structure, and functions of bacterial and fungal communities from a black-odorous river in Wuhu, China. Twenty-four samples were collected, and the diversity and structure of fungal and bacterial communities were determined by high-throughput sequencing. Proteobacteria and Rozellomycota were the main phyla in the bacterial and fungal communities, respectively. The results showed different distribution patterns of bacterial and fungal communities along the river. Physicochemical factors and heavy metals exhibited different effects on microbial variation. Specifically, pH and Cr negatively affected bacterial α-diversity, whereas total phosphorus and Cr significantly affected fungal α-diversity. Variance partitioning analysis revealed that physicochemical factors explained more of the bacterial community structure than heavy metals (49.5% vs. 36.6%), with pH and total phosphorus being the dominant factors. Opposite patterns were observed for fungal community structure, with heavy metals contributing the most (48.0%). A similar influence pattern was observed for the predicted functions of the two communities. This study suggests that heavy metals in eutrophication rivers are essential factors that shift the microbial variation and should be considered in urban river evaluation and remediation.

Bacterial Community Structure and Predicted Metabolic Function of Landfilled Municipal Solid Waste in China

The biodegradation behavior of municipal solid waste (MSW) depends on the diversity and metabolic function of bacterial communities, which are affected by environmental factors. However, the diversity of the bacterial communities and metabolic functions in MSW, as well as their influencing factors, remain unclear. In deep-aged MSW, the abovementioned deficiencies are more significant, and will effectively hamper landfill disposal. In this study, high-throughput sequencing was performed to examine the bacterial community structure and metabolic function from depths of 10 m to 40 m, of two large MSW landfills on the southeast coast of China. Thermotogota (1.6–32.0%), Firmicutes (44.2–77.1%), and Bacteroidota (4.0–34.3%) were the three dominant phyla among the 39 bacterial phyla identified in aged MSW samples. Bacterial genera associated with the degradation of many macromolecules, e.g., Defluviitoga, Hydrogenispora, and Lentimicrobium were abundantly detected in MSW samples, even in aged MSW. Redundancy analysis (RDA) showed that bacterial diversity in the landfills was most strongly correlated with electrical conductivity, age, and moisture content of the MSW. Tax4fun2 analysis predicted that there were abundant metabolism functions in aged MSW, especially functional enzymes (e.g., glycine dehydrogenase and cellulase) related to amino acids and cellulose degradation. This study increases our understanding of the bacterial diversity and functional characteristics in landfilled MSW.

Effect of feeding geese in cornfields on soil bacterial diversity and metabolic function

Feeding geese in cornfields may alter the composition and function of bacterial communities, which is pivotal for the improvement of sustainable soil fertility and the development of poultry-crop integrative agriculture. In a goose-fed field, the composition of the soil bacterial community was analysed using high-throughput sequencing and metabolic function (Biolog® Ecoplate™ microplate technology method). The relative abundance of beneficial bacteria, such as Fusarium and Pseudallescheria, in the goose-feeding soil was higher than that in the control. Linear discriminant analysis showed that Flavobacteriaceae was a unique landmark bacterium in the soil under the goose-feeding treatment. Based on PICRUSt prediction and Biolog-Eco analysis, the metabolic capacity of soil bacteria under the goose-feeding treatment was stronger than that of the control. A redundancy analysis showed that the alteration of soil bacterial community composition under the goose-feeding treatment was positively correlated with soil nutrients. Therefore, goose feeding led to more abundant bacterial families being involved in the nutrient cycle than it did in the control.

Succession of endophytic bacterial community and its contribution to cinnamon oil production during cinnamon shade-drying process

Cinnamon oil is a blend of secondary metabolites and is widely used as spice. Endophytic bacteria are always related to the secondary metabolites production. However, the potential of endophytic bacteria communities for cinnamon oil production during cinnamon shade-drying process is still not clear. In this study, we investigated the composition and metabolic function of endophytic bacterial community during 80-day shade-drying process. The temporal dynamics of essential oil content and its dominant constituents were analyzed. The succession of endophytic bacterial community from d0 to d80 was identified. The influence of endophytic bacterial community evolution on cinnamon oil is significant positive. Predictive functional analysis indicated that shade-drying process was rich in Saccharopolyspora that produce enzymes for the conversion of phenylalanine to cinnamaldehyde. These findings enhance our understanding of the functional bacterial genera and functional genes involved in the production of cinnamon oil during cinnamon shade-drying process.

Evidence of functional and structural changes in the microbial community beneath a succulent invasive plant in coastal dunes

Abstract Coastal dunes represent priority habitats for conservation due to the provision of valuable ecosystem services such as land protection, water supply or biodiversity conservation. Soil microbial communities are of crucial importance to maintain plant diversity due to harsh environmental conditions, water limitation and nutrient scarcity. Invasive alien plants represent a major threat to ecosystem conservation. Here, we explored different impacts of Carpobrotus edulis, a succulent plant invading coastal areas worldwide, on the function and structure of bacterial communities. Sand represents a challenging substrate due to low organic matter content and limited microbial activity. We optimized bacterial extraction for functional evaluation before assessing ecosystem impacts produced by C. edulis. We compared 12 extracting procedures combining different soil storage, sample amount and extracting solutions on the functional activity of sand communities through the community-level physiological profile. We further explored the function (using Biolog Ecoplates) and structure [using polymerase chain reaction–denaturing gradient gel electrophoresis (PCR-DGGE)] of bacterial communities from dunes invaded by C. edulis. Saline solution consistently increased bacterial cells detected by cytometry (P ≤ 0.001). Principal component analysis suggested a limited temporal framework (0–24 h) in which community function can be explored without significant alterations in C substrate consumption. Changes under C. edulis invasion exhibited a different pattern of C substrate utilization comparing native and non-native zones (interspecific), but also between native zones (intraspecific), suggesting that functional impacts are site-dependent. Complementary, results obtained from PCR-DGGE indicated that the bacterial community structure of native dunes significantly differed from dunes invaded by C. edulis.

Overlying water fluoride concentrations influence dissolved organic matter composition and migration from pore water in sediment via bacterial mechanisms

Fluoride (F−) is widespread in aquatic environments; however, it is not clear whether the fluctuation of F− concentrations in overlying lake water affects the composition and migration of dissolved organic matter (DOM) from sediment. A case study was presented in Sand Lake, China, and an experiment was conducted to analyze the influence of different F− concentrations in overlying water on DOM characteristics. Diffusion resulted in similarities in DOM components between overlying and pore waters, and bacterial activities and enzyme variation resulted in differences between them. Higher F− concentrations in overlying water resulted in a higher pH of pore water, which favored the enrichment of protein-like substances. Higher F− concentrations caused lower DOM concentrations and lower maximum fluorescence intensities (Fmax) of protein-like components in pore water. The F− concentrations had significantly negative correlations with Shannon indexes (P < 0.05). Thiobacillus influenced the migration of tyrosine-like substances by decreasing the pH of pore water. Trichococcus and Fusibacter altered the Fmax of protein-like, humic-like, and fulvic-like substances. The F− concentrations affected the DOM composition and migration due to the response of functional bacterial communities, which were positively correlated with the relative abundance of Thiobacillus and negatively correlated with the relative abundances of Trichococcus and Fusibacter. The high F− concentrations influenced the biosynthesis and degradation of protein-like substances by shifting the abundances of the relevant enzymes. The results of this study may provide ideas for investigating DOM cycling under the influence of F−, especially in lakes with fluctuations in F− concentrations.

High salinity slowed organic acid production from acidogenic fermentation of kitchen wastewater by shaping functional bacterial community

The high salinity of kitchen wastewater might have adverse effects on the production of short-chain fatty acids (SCFAs) in anaerobic fermentation. The effects and mechanisms of salinity on SCFA production in the anaerobic fermentation of kitchen wastewater were studied by varying the salt concentration, as follows: 0 g/L (S0), 2 g/L (S2), 6 g/L (S6), 10 g/L (S10), 15 g/L (S15), and 20 g/L (S20). Experimental results showed that hypersaline conditions (>10 g NaCl/L) accelerated the release of soluble proteins at the initial stage of anaerobic fermentation. They also significantly prohibited the hydrolysis and degradation of soluble proteins and carbohydrates. Compared with low salinity tests, the SCFA concentrations under hypersaline conditions (>10 g NaCl/L) only reached approximately 43% of the highest concentration on day 10, although the SCFA concentrations in all tests were very close on day 10 (14 g COD/L). High salinity delayed the production of n-butyric acid but did not change the composition of the total SCFAs. High salinity enriched Enterococcus and Bifidobacterium, the relative abundance levels of which reached 27.57% and 49.71%, respectively, before the depletion of substrate. High salinity showed a negative correlation with the relative abundance of the genera Clostridium_sensu_stricto_1, Prevotella and unclassified_f_Oscillospiraceae which are responsible for SCFA production. This study provided a theoretical basis for the fficient utilization of kitchen wastewater.

Contrasting summer versus winter dynamic microbial communities and their environmental driving factors in the solid-state saccharification process of Fuyu-flavor Baijiu

The seasonal spontaneous fermentation depends on the assembly of specific microbiota. However, a knowledge gap remains regarding the seasonal dynamics of microbial community and functionality. This study aimed to investigate the differences in microbial community dynamics during the saccharification process of Fuyu-flavor Baijiu in winter versus summer by employing high-throughput sequencing. It also explored the driving effects of environmental variables on the microbial succession. The environmental temperature of saccharification in summer (29 ± 1 °C) was strikingly different in winter (14 ± 1 °C), leading to a longer incubation time in winter fermentation. The dominant bacterial genera displayed in the early stage of the summer saccharification process were Staphylococcus, unclassified Enterobacteriaceae, and Weissella, whereas the dominant genus was Weissella during the middle stage and Lactobacillus during the late stage of saccharification. In contrast, unclassified Enterobacteriaceae and Weissella were dominant genera throughout the winter saccharification process. In the fungal community, Rhizopus was the dominant genus in summer and winter saccharification. Principal coordinate analysis revealed that the changes in the environmental temperature in winter versus summer had distinct impacts on the microbial community structure. Also, temperature was the key factor driving the succession of bacterial community, whereas pH was the main factor driving the succession of dominant fungi. Predictive gene functionality of bacterial and fungal communities was computed using the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States 2 against Kyoto Encyclopedia of Genes and Genomes (KEGG) database and MetaCyc database, respectively. Correlation networks were constructed to better understand the relationships between dominant microbial genera and physicochemical factors during the saccharification process. These results provided new insights into the Baijiu fermentation technology and allowed a theoretical basis for exploring effective management strategies regarding traditional fermentation in response to complex seasonal factors.

Polyamine-producing Bacteria Regulated the Community Structure of Rhizosphere Bacteria and Reduced the Absorption of Cd in Wheat

Some functional microorganisms in the soil immobilize heavy metals by adsorption and precipitation, prevent the absorption of heavy metals by crops, and play an important role in the passivation and remediation of medium and mild heavy metal-contaminated soil. A pot experiment was conducted to study the effects of the exogenous polyamine-producing bacterium Bacillus sp. N3 on Cd uptake and the bacterial community composition and function in the rhizosphere soil. The results showed that strain N3 significantly reduced the contents of Cd (64.7%) in wheat grain and DTPA-Cd (50.1%) in rhizosphere soil and increased the pH (from 6.84 to 6.97) and polyamine content. High-throughput sequencing results showed that inoculation of strain N3 reduced the diversity of the bacterial community; however, it increased the relative abundances of β-Proteobacteria, Bacteroidetes, and Firmicutes in wheat rhizosphere soil. Meanwhile, strain N3 also increased the relative abundances of heavy metal-immobilizing bacteria and plant growth-promoting bacteria (Bacillus, Arthrobacter, Brevundimonas, Ensifer, Pedobacter, Rhizobium, Pseudomonas, Enterobacter, and Serratia) in wheat rhizosphere soil. The PICRUSt function prediction showed that strain N3 increased the copy number of genes involved in antioxidant capacity, hormone synthesis, and sulfur metabolism in wheat rhizosphere soil. These results indicated that the polyamine-producing bacteria N3 reduced the DTPA-Cd content by increasing the pH; the polyamine contents; the abundances of bacteria with heavy metal-immobilizing or plant growth-promoting traits; and the metabolic pathway involved in antioxidant capacity, hormone synthesis, and sulfur metabolism in wheat rhizosphere soil, thus inhibiting the absorption of Cd by wheat. The results provide theoretical basis and technical support for restoring farmland with excessive heavy metals and ensuring the safe production of wheat.

Deciphering the dominant components and functions of bacterial communities for lignocellulose degradation at the composting thermophilic phase

The decomposition and transformation of organic matters during composting process are performed by various microorganisms. However, the bacterial communities and their functions usually vary with composting materials. Here the dominant bacterial genera and their functions were identified at the thermophilic phase during composting of mulberry branches with silkworm excrement (MSE), pig manure (MPM) and cow manure (MCD). The activities of β-glucosidase and endoglucanase were highest for MCD (1.31 and 17.15 µg g−1 min−1) and lowest for MPM (0.92 and 14.22 µg g−1 min−1). Random Forest model and correlation analysis revealed that Stenotrophomonas, Bacillus, and Sinibacillus were the dominant bacterial genera involved in lignocellulose degradation regardless of composting materials. Carbohydrate metabolism, amino acid metabolism, and DNA replication and repair were primary functions of the bacterial communities for the three types of composting. The quantification of lignocellulose degradation genes further verified the dominant functions of the bacterial communities.

Soil pH: a key edaphic factor regulating distribution and functions of bacterial community along vertical soil profiles in red soil of pomelo orchard

BackgroundSoil microbes exist throughout the soil profile and those inhabiting topsoil (0–20 cm) are believed to play a key role in nutrients cycling. However, the majority of the soil microbiology studies have exclusively focused on the distribution of soil microbial communities in the topsoil, and it remains poorly understood through the subsurface soil profile (i.e., 20–40 and 40–60 cm). Here, we examined how the bacterial community composition and functional diversity changes under intensive fertilization across vertical soil profiles [(0–20 cm (RS1), 20–40 cm (RS2), and 40–60 cm (RS3)] in the red soil of pomelo orchard, Pinghe County, Fujian, China.ResultsBacterial community composition was determined by 16S rRNA gene sequencing and interlinked with edaphic factors, including soil pH, available phosphorous (AP), available nitrogen (AN), and available potassium (AK) to investigate the key edaphic factors that shape the soil bacterial community along with different soil profiles. The most dominant bacterial taxa were Proteobacteria, Acidobacteria, Actinobacteria, Chloroflexi, Crenarchaeota, and Bacteriodetes. Bacterial richness and diversity was highest in RS1 and declined with increasing soil depth. The distinct distribution patterns of the bacterial community were found across the different soil profiles. Besides, soil pH exhibited a strong influence (pH ˃AP ˃AN) on the bacterial communities under all soil depths. The relative abundance of Proteobacteria, Actinobacteria, Crenarchaeota, and Firmicutes was negatively correlated with soil pH, while Acidobacteria, Chloroflexi, Bacteriodetes, Planctomycetes, and Gemmatimonadetes were positively correlated with soil pH. Co-occurrence network analysis revealed that network topological features were weakened with increasing soil depth, indicating a more stable bacterial community in the RS1. Bacterial functions were estimated using FAPROTAX and the relative abundance of functional bacterial community related to metabolic processes, including C-cycle, N-cycle, and energy production was significantly higher in RS1 compared to RS2 and RS3, and soil pH had a significant effect on these functional microbes.ConclusionsThis study provided the valuable findings regarding the structure and functions of bacterial communities in red soil of pomelo orchards, and highlighted the importance of soil depth and pH in shaping the soil bacterial population, their spatial distribution and ecological functioning. These results suggest the alleviation of soil acidification by adopting integrated management practices to preserve the soil microbial communities for better ecological functioning.

Assessing synergistic effects of crop rotation pattern, tillage practice, and rhizosphere effect on soil bacterial community structure and assembly in China's Loess Plateau farmlands

Soil bacterial communities are important soil regulators in agroecosystems. However, few studies have investigated the influences of integrated agricultural management practices on farmland soil bacterial community diversity and assembly processes. In this study, we assessed the impact of crop species (maize and soybean), tillage practice (chisel plow tillage, CPT; zero tillage, ZT; plow tillage, PT), rhizosphere effect (rhizosphere and bulk soils), and their interactions on the soil bacterial communities in Loess Plateau farmlands. Conservation tillage significantly increased soil moisture (SM), clay and sand fractions, and carbon and nitrogen levels; whereas silt fraction and pH decreased. Rhizosphere effect significantly improved soil texture and decreased SM, pH, total nitrogen, and nitrate nitrogen. Soybean cultivation significantly increased SM, silt fraction, and pH; while clay fraction decreased. Additionally, the rhizosphere effect decreased the competition among rhizosphere bacterial communities (edges: rhizosphere = 926, bulk = 1095; density: rhizosphere = 0.157, bulk = 0.184) and increased the structural complexity of the community network (modularity: rhizosphere = 0.857, bulk = 0.556); moreover, conservation tillage and soybean cultivation increased community network complexity (modularity: CPT = 0.879, ZT = 0.742, PT = 0.495; maize = 0.525, soybean = 0.888). Although the phylogenetic clustering of rhizosphere bacterial communities caused by the rhizosphere effect was lower than that of bulk soil bacterial communities (2.13%), it had no significant influence on rhizosphere or bulk soil bacterial community assembly, and deterministic processes dominated the formation of soil bacterial community structure. In conclusion, clarifying the variations in soil bacterial communities under integrated agricultural management practices can help predict trends in soil bacterial community function which can, in turn, effectively guide biological management decision-making in farming operations. Our findings may provide additional insights into the underground processes in farmland and facilitate the development of conservation farming operations as sustainable agricultural practices.

Soil Microbial Community Response to Nitrogen Application on a Swamp Meadow in the Arid Region of Central Asia.

Although a large number of studies have reported the importance of microbial communities in terrestrial ecosystems and their response to nitrogen (N) application, it is not clear in arid alpine wetlands, and the mechanisms involved need to be clarified. Therefore, the response of the soil microbial community in a swamp meadow to short-term (1 year) N application (CK: 0, N1: 8, N2: 16 kg⋅N⋅hm–2⋅a–1) was studied using 16S/ITS rRNA gene high-throughput sequencing technology. Results showed that N application had no significant effect on soil microbial community diversity, but significantly changed soil bacterial community structure. N1 and N2 treatments significantly reduced the relative abundance of Chloroflexi (18.11 and 32.99% lower than CK, respectively). N2 treatment significantly reduced the relative abundance of Nitrospirae (24.94% lower than CK). Meanwhile, N application reduced the potential function of partial nitrogen (N) and sulfur (S) cycling in bacterial community. For example, compared with CK, nitrate respiration and nitrogen respiration decreased by 35.78–69.06%, and dark sulfide oxidation decreased by 76.36–94.29%. N application had little effect on fungal community structure and function. In general, short-term N application directly affected bacterial community structure and indirectly affected bacterial community structure and function through available potassium, while soil organic carbon was an important factor affecting fungal community structure and function.

Rare-earth metal oxide nanoparticles decouple the linkage between soil bacterial community structure and function by selectively influencing potential keystone taxa

Excessive production and application of rare-earth metal oxide nanoparticles warrants assessment of their environmental risks. Little is known about the impact of these nanoparticles on soil bacterial communities. We quantified the effects of nano-Gd2O3 and nano-La2O3, at the different concentrations and exposure regimes, on soil bacterial community structure and function as well as the structure-function relationship. Further, we constructed and analyzed a co-occurrence network to identify and characterize potential keystone taxa that were related to the enzyme activities and responded to the increasing concentrations of nanoparticles. Both nano-Gd2O3 and nano-La2O3 significantly altered the bacterial community structure and function in a concentration-dependent manner; however, these negative effects were observed on day 1 or day 7 but not on day 60, indicating that these effects were transient and the bacterial communities can mitigate the effect of these nanoparticles over time. Interestingly, the nanoparticle exposure decoupled the relationship between the structure and function of the soil bacterial communities. The decoupling was due to changes in the composition and relative abundances of potential keystone taxa related to bacterial community functions. Altogether, we provide insights into the interactions between the rare-earth metal oxide nanoparticles and soil bacterial communities. Our results facilitate the environmental risk assessment and safe usage of rare-earth metal oxide nanoparticles.

Maize root-associated niches determine the response variation in bacterial community assembly and function to phthalate pollution

Plant root-associated microbiome can be influenced by environmental stress like pollution. However, how organic pollution influences microbial communities in different root-associated niches and plant-microbe interaction remains unclear. We analyzed maize root-associated bacterial communities under stress of di-(2-ethylhexyl) phthalate (DEHP). The results demonstrate that structures and functions of bacterial communities are significantly different among four root-associated niches, and bacterial diversities gradually decline along bulk soil - rhizosphere - rhizoplane - endosphere. DEHP stress significantly reduces bacterial community diversities in both rhizosphere and rhizoplane, and changes their composition, enrichment and depleting process. DEHP stress led to the enrichment of some specific bacterial taxa like phthalate-degrading bacteria (e.g., Rhizobium and Agromyces) and functional genes involving in phthalate degradation (e.g., pht3 and pcaG). Notably, rhizoplane bacterial community is more sensitive to DEHP stress by enriching stress-resistant bacteria and more complex microbial network on rhizoplane than in rhizosphere. DEHP stress also disturbs the colonization and biofilm forming of root-associated bacteria on rhizoplane. Rhizoplane bacterial community is significantly correlated with maize growth while negatively influenced by DEHP stress. DEHP stress negatively influences plant-microbe interaction and inhibits maize growth. This study provides deep and comprehensive understanding for root-associated bacterial community in response to organic pollution.