Bacterial Community Function Research Articles

Effect of AM Fungi Inoculation on Litter Bacterial Community Characteristics under Heavy Metal Stress.

Because microorganisms are the primary driving force behind litter decomposition, they play an important role in maintaining ecosystem material and chemical cycling. Arbuscular mycorrhizal (AM) fungi can improve host plant tolerance to various environmental stressors, making their application in mining area remediation important. In this study, litter from the dominant plant species (Imperata cylindrica) in a copper tailings mining area was selected as the experimental material. We conducted a greenhouse-based heavy metal stress experiment to investigate how AM fungi affect litter microbial community characteristics and key ecological factors. Results showed that AM fungi species, heavy metal treatments, and their combined interaction had significant impacts on litter pH. Additionally, enzyme activities in litter were significantly affected by interactions between AM fungi species and heavy metal contaminates. Ralstonia was significantly positively correlated to lead (Pb) content, indicating that Ralstonia had a certain tolerance to Pb pollution. Sucrase and urease activity were increased when plants were inoculated with Rhizophagus irregularis under Pb stress. Furthermore, Microbacterium, Brevundimonas, and Pseudonocardia all may play important roles in litter decomposition, while a certain tolerance was observed in Kushneria and Roseivivax to heavy metal pollution when plants were inoculated with Glomus mosseae. Results showed that AM fungi affected litter bacterial community structure and function by influencing plant litter properties. By exploring interactions between AM fungi and bacterial communities in plant litter under heavy metal stress, we will better understand associative processes that promote the cycling of soil organic matter and nutrients contaminated by non-ferrous metal tailings.

Aeration increases soil bacterial diversity and nutrient transformation under mulching-induced hypoxic conditions

Soil oxygen (O2) deficiency induced by organic mulching is easy to overlook. Aeration has been shown to potentially alleviate soil hypoxia stress. However, the responses of soil bacterial communities to such mulching-induced hypoxic conditions and aeration remain elusive. Therefore, a three-year field experiment, consisting of mulching (T1), mulching with aeration (TA1, poor aeration; TA2, strong aeration), and no-mulching (CK) treatments, was conducted in bamboo (Phyllostachys praecox) plantations. According to our results, the strong aeration treatment (TA2) alleviated soil acidification, increased soil nutrient availability, and significantly increased soil O2 content by 18.44% (P < 0.05) when compared with T1. In addition, TA2 significantly increased soil β-glucosidase, invertase, urease, and acid phosphatase activities compared with CK and T1 (P < 0.05). The alpha diversity indices with TA2 treatment were the highest, indicating that aeration increased the species richness and diversity of bacteria. The changes in bacterial community composition associated with TA2 treatment (i.e., an increase in Firmicutes, Verrucomicrobia, and Faecalibacterium abundance and a decrease in Chloroflexi and Bradyrhizobium abundance) were mainly related to nutrient and O2 content. Mantel Test results suggested that soil O2 content and temperature were the key factors shaping bacterial community composition. Structural equation modeling revealed that soil O2 content had a positive and direct influence on bacterial community diversity. Functional annotation of prokaryotic taxa predicted that TA2 significantly increased the relative abundance of bacterial communities associated with nitrification, nitrogen fixation, and ureolysis. Our results demonstrated that optimal soil aeration conditions (17.60% of O2 content) could enhance the diversity and function of soil bacterial communities. Overall, the findings of this study could serve as a benchmark for alleviating soil hypoxia caused by organic mulches, which is important for increasing the functionality of nutrient cycling bacterial communities in the soil.

Identification of root bacteria associated with different stripe rust resistance in wheat cultivars

AbstractThe plant rhizosphere bacterial community influences plant stress resistance. Stripe rust causes severe damage to wheat (Triticum aestivum L.) production. To reveal the composition and function of root bacterial communities in wheat cultivars with different stripe rust resistance, rhizosphere soil samples were collected from four wheat cultivars. High‐throughput 16S rRNA gene sequencing was used to study the rhizobacterial community structure and function in stripe rust‐resistant (Guinong 19 and Huamai 1223) and ‐susceptible (Mingxian 169 and Taichung 29) wheat cultivars. A total of 6,392 operational taxonomic units (OTUs) were detected, belonging to 29 bacterial phyla. Analysis showed the susceptible and resistant wheat cultivars had different microbial communities. Principal coordinate analysis showed that all wheat rhizosphere bacterial samples could be divided into two groups, according to different disease resistance. Linear discriminant analysis effect size analysis showed that different bacterial taxa were enriched in the rhizosphere soil between resistant and susceptible wheat cultivars. Functional analysis showed that the bacterial community in stripe rust‐resistant wheat had greater amino acid transport and metabolic functions. Our research not only provides basic knowledge of the composition of wheat‐related microbiota but also reveals the microbial taxa that could be integrated into the management strategy of wheat stripe rust.

Whole-Genome Duplication and Host Genotype Affect Rhizosphere Microbial Communities.

ABSTRACTThe composition of microbial communities found in association with plants is influenced by host phenotype and genotype. However, the ways in which specific genetic architectures of host plants shape microbiomes are unknown. Genome duplication events are common in the evolutionary history of plants and influence many important plant traits, and thus, they may affect associated microbial communities. Using experimentally induced whole-genome duplication (WGD), we tested the effect of WGD on rhizosphere bacterial communities in Arabidopsis thaliana. We performed 16S rRNA amplicon sequencing to characterize differences between microbiomes associated with specific host genetic backgrounds (Columbia versus Landsberg) and ploidy levels (diploid versus tetraploid). We modeled relative abundances of bacterial taxa using a hierarchical Bayesian approach. We found that host genetic background and ploidy level affected rhizosphere community composition. We then tested to what extent microbiomes derived from a specific genetic background or ploidy level affected plant performance by inoculating sterile seedlings with microbial communities harvested from a prior generation. We found a negative effect of the tetraploid Columbia microbiome on growth of all four plant genetic backgrounds. These findings suggest an interplay between host genetic background and ploidy level and bacterial community assembly with potential ramifications for host fitness. Given the prevalence of ploidy-level variation in both wild and managed plant populations, the effects on microbiomes of this aspect of host genetic architecture could be a widespread driver of differences in plant microbiomes.IMPORTANCE Plants influence the composition of their associated microbial communities, yet the underlying host-associated genetic determinants are typically unknown. Genome duplication events are common in the evolutionary history of plants and affect many plant traits. Using Arabidopsis thaliana, we characterized how whole-genome duplication affected the composition of rhizosphere bacterial communities and how bacterial communities associated with two host plant genetic backgrounds and ploidy levels affected subsequent plant growth. We observed an interaction between ploidy level and genetic background that affected both bacterial community composition and function. This research reveals how genome duplication, a widespread genetic feature of both wild and crop plant species, influences bacterial assemblages and affects plant growth.

Distant somatic hybridization alters the structure of wheat root bacterial microbiota

AbstractRoot microbiota affect the host plant's adaptation to adverse environments. The structure and function of plant root bacterial communities are affected by soil physicochemical properties and plant genotypes. Distant hybridization is a common breeding strategy to introgress the excellent genes of wild relatives into the crop genome. The effect of distant hybridization on the crop root microbiota has not been reported. In this study, the structure and function of root bacterial community of the somatic hybrid wheat introgression lines SR3 and SR4, which have been respectively reported to be tolerant to salt and saline‐alkali stress, and their parent wheat cultivar JN177 as well as common wheat cultivar Chinese Spring (CS) were analyzed using 16S rRNA high‐throughput sequencing technology. The results showed that distant hybridization altered the structure and function of wheat (Triticum aestivum L.) root bacterial community. Compared with the parent JN177, some bacterial genera related to plant growth and stress resistance showed higher abundance in SR3 and SR4. Intriguingly, compared with parent JN177, the root bacterial communities of SR3 and SR4 are more similar to that of CS. This indicated that the process of distant hybridization may alter key genes regulating wheat root microbiota.

Analysis on the Structure and Function of the Bacterial Community in the Replanting Soil of Basswood of Ganoderma lingzhi Medicinal Mushroom (Agaricomycetes).

This study aimed to investigate the impact of the replanting of basswood Ganoderma lingzhi on the soil bacterial community and reveal the obstacle phenomenon of replanting basswood G. lingzhi. In this study, the soil bacterial community of wild 20 cm (N0a) and 40 cm deep soil (N0b), cultivated once (N1a, N1b) and twice (N2a, N2b), were investigated by Illumina MiSeq sequencing. The predominant bacterial phyla at the phylum classification level were Acidobacteria, Chloracidobacteria, Nitrospira, Spartobacteria, Gemmatimonadetes, Acidobacteria-6. Still, only the relative abundance of Chloracidobacteria and Acidobacteriia increased after two years of replanting of basswood G. lingzhi. At the genus level, the dominant genus included many unclassified bacteria. Among the known genera, the best genus was DA101, which showed a decreasing trend after two years of replanting. Network analysis showed that more connections of bacterial communities were observed in soil samples of the group "a," indicating that the replanting of basswood G. lingzhi can affect the relationship between soil bacterial communities at depths. The phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) analysis showed that the gene metabolism function of soil bacteria was quite different after one year of replanting basswood G. lingzhi. The replanting of basswood G. lingzhi changed the composition and function of the soil bacterial community, and also affected the bacterial community diversity in the soil at different depths.

Effects of enrichmemt planting with native tree species on bacterial community structure and potential impact on Eucalyptus plantations in southern China

Multi-generational planting of Eucalyptus species degrades soil quality but the introduction of legumes can improve soil fertility and microbial diversity. However, the effects of introducing non-legume native tree species on soil nutrients and bacterial community structure remain poorly understood. This study investigated the impacts of the conversion of third generation monoculture Eucalyptus plantations to mixed systems including Eucalyptus urograndis with Cinnamomum camphora (EC) and E. urograndis with Castanopsis hystrix (EH), on soil chemical and biochemical properties and bacterial community structure, diversity and functions. First generation E. urophylla plantations were the control. Results show that planting the third generation Eucalyptus led to a significant decrease in pH, organic matter, nutrient content, enzyme activities (invertin, acid phosphataes, and urease), and bacterial α-diversity compare to the controls. However, the mixed planting showed significant improvement in soil chemical and biochemical attributes and bacterial α-diversity, although the E. urograndis and C. hystrix planting had no improvement. Chloroflexi (oligotrophic bacteria) were significantly enriched in third generation Eucalyptus and Eucalyptus + C. hystrix, while proteobacteria increased significantly in the E. urograndis with C. camphora plantings. The relative abundance of multiple metabolic pathways increased significantly in the third generation Eucalyptus plantations whereas membrane transport-related genes were enriched in soils of the mixed systems. The changes in bacterial community structures in the two mixed systems were driven by diversity, organic matter and acid phosphatase, while bacterial functions were affected by invertase, {mathrm{NO}}_{3}^{-}-N, diversity and urease. These results suggest that the transformation of successive monoculture Eucalyptus plantations into mixed plantations reduces the depletion of soil nutrients and enhances the ecological function of soil microorganisms.

Effects of Ship Navigation Disturbance on Sediment Bacterial Community Structure and Function: Relative Contributions of Perfluoroalkyl Acids and Physicochemical Parameters

Effects of Ship Navigation Disturbance on Sediment Bacterial Community Structure and Function: Relative Contributions of Perfluoroalkyl Acids and Physicochemical Parameters

种植模式和坡位对茶园土壤细菌群落结构及功能类群的影响

PDF HTML阅读 XML下载 导出引用 引用提醒 种植模式和坡位对茶园土壤细菌群落结构及功能类群的影响 DOI: 10.5846/stxb202110122879 作者: 作者单位: 作者简介: 通讯作者: 中图分类号: 基金项目: 福建省自然科学基金项目（2021J01489）；国家重点研发计划项目（2016YFD0200903）；福建省科技厅公益类科研专项（2021R1029002）；中央引导地方科技发展专项（2020L3030） Effects of planting patterns and slope positions on soil bacterial community structure and functional groups in tea gardens Author: Affiliation: Fund Project: the Natural Science Foundation of Fujian Province,China(2021J01489)；the National Key Research and Development Program of China (2016YFD0200903)；；Special Founds Projects for Basic Scientific Research of Public Welfare in Fujian Province(2021R1029002);Special Program for Science and Technology Development of Fujian Province from the Ministry of Science and Technology of China(2020L3030) 摘要 | 图/表 | 访问统计 | 参考文献 | 相似文献 | 引证文献 | 资源附件 | 文章评论 摘要:茶树（Camellia sinensis L.）种植是亚热带丘陵山区主要的土地利用类型，茶园种植模式是影响土壤细菌群落结构的主要人为因素。为揭示种植模式和坡位对土壤细菌群落结构和功能的影响，选取两种不同种植模式（常规和有机种植模式）和3个坡位（上、中、下坡位）表层土壤（0-20cm）为对象，采用野外调查、Illumina Miseq高通量测序和PICRUSt2功能预测相结合的研究方法，研究不同种植模式和坡位下土壤细菌群落结构和功能特征，阐明土壤理化性质对土壤细菌群落结构的影响，预测土壤细菌功能特征。研究结果表明：（1）与常规种植模式相比，有机种植模式茶园土壤细菌Alpha多样性有所降低，其中中坡位常规茶园土壤细菌Sobs和Simpson指数显著高于有机茶园（P<0.05）；从坡面尺度看，两种种植模式下土壤细菌Alpha多样性指标均以中坡位最高，其中常规茶园中坡位土壤细菌Ace和Simpson指数均显著高于下坡位（P<0.05）。（2）各样地茶园土壤细菌共获得29个门82个纲190个目316个科517个属929个种，主要细菌优势门为绿弯菌门（Chloroflexi）、放线菌门（Actinobacterita）、变形菌门（Proteobacteria）、酸杆菌门（Acidobacteria）。土壤细菌群落优势属以AD3、热酸菌属（Acidothermus）、norank_f__norank_o__Elsterales和norank_f__Xanthobacteraceae为主。（3）主坐标分析（PCoA）显示，不同种植模式的茶园土壤细菌群落结构存在明显差异，常规种植模式下不同坡位之间的土壤细菌群落结构有显著差异（P<0.05），有机种植下不同坡位之间的土壤细菌群落结构无显著差异。置换多元方差分析（PERMANOVA）结果表明不同种植模式的土壤细菌群落结构差异显著（P<0.05），而不同坡位土壤细菌群落结构无显著差异（P>0.05），说明种植模式对茶园土壤细菌群落结构的影响更大。组间群落差异分析（LEfSe）表明，57个差异物种对种植模式非常敏感，不同种植模式富集了不同的细菌类群。（4） PICRUSt2功能预测共获得6个一级功能层和46个二级功能层，表现出功能上的丰富性，土壤细菌群落在代谢、遗传信息处理和环境信息方面功能活跃。有机种植模式提高了土壤细菌碳水化合物代谢、氨基酸代谢、膜运输、信号转导、脂质代谢及外源生物降解与代谢功能。（5）相关分析和冗余分析结果表明，土壤碱解氮、速效磷、全磷、全钾和pH是影响土壤细菌群落丰度和多样性的主要影响因子。总体而言，有机种植模式改变了茶园土壤细菌群落结构和代谢功能，增加土壤有益细菌的数量，有利于保持茶园土壤可持续的生态环境。 Abstract:Tea (Camellia sinensis L.) is one of the most important and traditional economic crops widely cultivated in acid red soils in the subtropical zones in China, and the planting pattern constitutes the major artificial factor affecting the soil bacterial community structure. However, the effect of the planting patterns on soil bacterial community structures and functions in the tea garden remains unclear. To study the characteristics of soil bacterial community compositions and functional groups under different planting patterns and slope positions, soil samples derived from topsoil (0-20cm) were collected from the upper, middle, and lower slope positions of conventional (CT) and organic (OT) tea gardens. Illumina MiSeq sequencing and PICRUSt2 predictions were performed to investigate the bacterial community structures and functional groups, respectively. Further, the Spearman correlation analysis and redundancy analysis (RDA) were also used to examine the soil property factors that drived the community structure. The results showed that:(1) compared with the conventional planting pattern, the soil bacterial diversity under organic planting pattern decreased remarkably, and the Sobs and Simpson indices significantly decreased in the middle slope position (P<0.05). Regardless of the planting patterns, the soil bacterial diversities were the highest in the middle slope position. Ace and Simpson indices of the bacterial community in this slope position were significantly higher than the respective values of the lower slope position under the conventional planting pattern (P<0.05). (2) A total of 29 phyla, 82 classes, 190 orders, 316 families, 517 genera and 929 species were detected in soil bacteria of tea gardens. The dominant bacterial phyla were Chloroflexi, Actinobacterita, Proteobacteria and Acidobacteria. The dominant bacterial genera were AD3, Acidothermus, norank_f__norank_o__Elsterales, and norank_f__Xanthobacteraceae. (3) The results of principal coordinates analysis (PCoA) showed that the soil bacterial community structures could be distinctly separated in different planting patterns. The community structures of soil bacteria in different slope positions were significantly different under the conventional planting pattern (P<0.05), whereas they were similar under the organic planting pattern. The permutational multivariate analysis of variance (PERMANOVA) indicated that the bacterial community structures under different planting patterns showed significant differences (P<0.05), whereas those in different slope positions did not (P>0.05). The linear discriminant analysis effect size (LEfSe) analysis showed that 57 biomarkers were very sensitive to the planting patterns, with different planting patterns enriching different bacterial populations. (4) PICRUSts2 platform predicted 6 biological metabolic pathways and 46 subfunctions in the soil bacteria of tea gardens, suggesting of abundant soil bacterial functions. These pathways mainly involved metabolic processes, genetic information processing, and environmental information processing. The organic planting pattern increased carbohydrate metabolism, amino acid metabolism, membrane transport, signal transduction, and lipid metabolism of cofactors and vitamins functional genes. (5) The results of the Spearman correlation analysis and RDA showed that soil alkaline nitrogen, available phosphorus, total phosphorus, total potassium and pH were the main factors affecting the abundance and diversity of the soil bacterial community. In conclusion, the organic planting changes the community structure and the metabolic functions of soil bacteria, promotes soil bacteria carbon and nitrogen metabolism and enriches beneficial bacteria, and thus is beneficial to maintain the sustainable ecosystem in tea garden soil. 参考文献 相似文献 引证文献

Multi-Omics Eco-Surveillance of Bacterial Community Function in Legacy Contaminated Estuary Sediments

Multi-Omics Eco-Surveillance of Bacterial Community Function in Legacy Contaminated Estuary Sediments

Deciphering the characterization, ecological function and assembly processes of bacterial communities in ship ballast water and sediments

Various microorganisms are transported worldwide via the water and sediments inside ship ballast tanks. Nevertheless, the ecological functions and assembly processes of bacterial communities in ballast water and sediments remain poorly understood. Here, we investigated the bacterial composition, community assembly processes, and putative functions through analyses of 70 ballast water and sediment samples obtained from various ships. The results showed that the ballast sediments contained a higher diversity of bacterial communities, whereas the ballast water was characterized by the dominance of Proteobacteria. Both the composition and potential function structures of bacterial communities were clearly different between the ballast water and sediment samples. The ballast water exhibited an abundance of microorganisms that involved in sulfur oxidation, whereas the bacterial species associated with nitrogen metabolism were abundant in the sediments. Co-occurrence network analysis revealed that the communities in ballast sediment samples possessed more complex network structures with higher modularity and positive associations among bacterial populations. Stochastic processes, especially the dispersal limitation process played the most important influence in the assembly of the communities in ballast water. Meanwhile, the bacterial communities in the ballast sediments were primarily governed by the homogeneous selection of determinacy. The results from this study will help us understand the ecological processes related to the bacterial communities in the ballast tanks and provide a foundation for the management of ballast water and sediments.

Soil Bacterial and Fungal Community Responses to Throughfall Reduction in a Eucalyptus Plantation in Southern China

In subtropical plantations in southern China, how soil microbial communities respond to climate change-induced drought is poorly understood. A field experiment was conducted in a subtropical Eucalyptus plantation to determine the impacts of 50% of throughfall reduction (TR) on soil microbial community composition, function, and soil physicochemical properties. Results showed that TR reduced soil water content (SWC) and soil available phosphorus (AP) content. TR significantly altered 196 bacterial operational taxonomic units (OTUs), most of them belonging to Acidobacteria, Actinobacteria, and Proteobacteria, while there were fewer changes in fungal OTUs. At the phylum level, TR increased the relative abundance of Acidobacteria at 0–20 cm soil depth by 37.18%, but failed to influence the relative abundance of the fungal phylum. Notably, TR did not alter the alpha diversity of the bacterial and fungal communities. The redundancy analysis showed that the bacterial communities were significantly correlated with SWC, and fungal communities were significantly correlated with AP content. According to predictions of bacterial and fungal community functions using PICRUSt2 and FUNGuild platforms, TR had different effects on both bacterial and fungal communities. Overall, SWC and AP decreased during TR, resulting in greater changes in soil bacterial community structure, but did not dramatically change soil fungal community structure.

High-Throughput Sequencing Analysis of the Composition and Diversity of the Bacterial Community in Cinnamomum camphora Soil.

Soil bacterial communities and root-associated microbiomes play important roles in the nutrient absorption and healthy growth of host plants. Cinnamomum camphora is an important timber and special economic forest tree species in Fujian Province. In this study, the high-throughput sequencing technique was used to analyze the composition, diversity, and function of the bacterial communities present in the soil from different samples and slope positions of C. camphora. The results of this analysis demonstrated that the related bacterial communities in C. camphora soil were mainly clustered based on sample type. Bacterial alpha diversity in the rhizosphere and bulk soil of C. camphora growing downhill was higher than that of C. camphora growing uphill. At the phylum level, Bacteroidetes, Proteobacteria, Chloroflexi, and Gemmatimonadetes were positively correlated with pH, available phosphorus, total phosphorus, available potassium, and total potassium, while Acidobacteria and Verrucomicrobia were negatively correlated with alkaline-hydrolyzable nitrogen. These results show that there were remarkable differences in the composition, diversity, and function of related bacterial communities between different sample types of C. camphora soil. The slope position had a marked effect on the bacterial communities in the rhizosphere and bulk soil, while the root endosphere remained unaffected.

Toward a function-first framework to make soil microbial ecology predictive.

Soil microbial communities perform vital ecosystem functions, such as the decomposition of organic matter to provide plant nutrition. However, despite the functional importance of soil microorganisms, attribution of ecosystem function to particular constituents of the microbial community has been impeded by a lack of information linking microbial function to community composition and structure. Here, we propose a function-first framework to predict how microbial communities influence ecosystem functions. We first view the microbial community associated with a specific function as a whole and describe the dependence of microbial functions on environmental factors (e.g., the intrinsic temperature dependence of bacterial growth rates). This step defines the aggregate functional response curve of the community. Second, the contribution of the whole community to ecosystem function can be predicted, by combining the functional response curve with current environmental conditions. Functional response curves can then be linked with taxonomic data in order to identify sets of "biomarker" taxa that signal how microbial communities regulate ecosystem functions. Ultimately, such indicator taxa may be used as a diagnostic tool, enabling predictions of ecosystem function from community composition. In this paper, we provide three examples to illustrate the proposed framework, whereby the dependence of bacterial growth on environmental factors, including temperature, pH, and salinity, is defined as the functional response curve used to interlink soil bacterial community structure and function. Applying this framework will make it possible to predict ecosystem functions directly from microbial community composition.

Soil heavy metals and phytoremediation by Populus deltoides alter the structure and function of bacterial community in mine ecosystems

Despite the fact that microbes act as key indicators of soil heavy metal (HMs) toxicity, their variations and adaptation to the long-term HMs pollution in mine ecosystems, particularly field study knowledge of the effects of phytoremediation, remain insufficient. A comparative study on microbiota of the rhizosphere and endosphere of Populus deltoides and their structural and functional variations in response to composite HMs pollution was conducted. Results suggested that habitat niche was the driving force in shaping bacterial composition as shown by distinctive niche differentiation of 48 core species. Among all factors, HM explained 43% of the bacterial variability that constituted the key determinant for all microbiota structures. Further redundancy analysis revealed Cd and Pb were the main drivers of soil microbiota distribution, while none of HMs significantly affected the structure of endophytes. The responses of microbiota to HM stress varied in different habitats. The diversity (Shannon) and richness (Chao) of bare soil (CS) was significantly deteriorated by HM, but richness of rhizosphere (CRS) was greatly increased than CS, indicating the beneficial effects of phytoremediation to bacterial composition. Functional genes were also enriched in contaminated samples related to multiple cell defence mechanisms including extracellular binding, transmembrane transport, and antioxidant protection. Metabolic pathways related to plant signaling compounds and energy-rich nucleotides were enriched in endophytes, inferring the potential for stress protection and plant growth promotion. This study indicated that shifts of microbial organization and function strengthened their HM stress adaptability; plant associated microbiome contributed to the phytoremediation efficiency, which could provide the basis for soil evaluation after phytoremediation and further exploration of host-microbe interactions in mine ecosystems.

Insight into the organic matter degradation enhancement in the bioelectrochemically-assisted sludge treatment wetland: Transformation of the organic matter and microbial community evolution

Sludge treatment wetland (STW) has been widely used to dewater and mineralize the various sludge, but the low degradation ability of organic matter can limit its application. Bioelectrochemistry has been proven to accelerate the degradation of organic compounds and recover bioenergy from the sludge. In this study, a bioelectrochemical-assisted sludge treatment wetland (BE-STW) system was constructed to determine the most common types of degraded organic matter and the functional bacterial community. It was found that the bioelectrochemistry process contributed to a further removal of the total chemical oxygen demand (TCOD) by 19% (±0.6) and the additional soluble chemical oxygen demand (SCOD) value was 64.10% (±0.63), with a voltage output of 0.961 V and a power density of 0.351 W/m3. The hydrophilic and hydrophobic acid fractions of the sludge were preferentially removed in BE-STW. The tryptophan-like protein and fulvic acid-like substances were totally removed, whereas, the hydrolysis of aromatic organic compounds in the neutral and hydrophobic acid fractions was enhanced. Also, the enrichment of Longilinea and Methylophilus improved the hydrolysis of organic matter. Moreover, the high relative abundance of Thauera, Dechloromonas, and Syntrophorhabdus could accelerate the degradation of aromatic compounds in the BE-STW system. The bacteria from the genus Geobacter was predominantly detected (2.48%) in the anodic biofilm on BE-STW. The results showed that bioelectrochemistry could improve the sludge stabilization degree in STW, accelerate the organic matter degradation and hydrolysis efficiency, and harvest bioelectricity, simultaneously. This technology can provide a new pathway to increase the efficiency of the traditional STW systems.

Land-use change affects the diversity and functionality of soil bacterial communities in semi-arid Chaco region, Argentina

The semi-arid Chaco ecoregion has been heavily affected by the conversion of pastures to cropland. Our knowledge about the impact of land use change on soil microbial community diversity and functions in this region is limited. Here, we assessed the impact of different land uses and management practices (i.e.: ungrazed pasture, grazed pasture and cropping systems under zero and conventional tillage) on soil bacterial communities structure and functions, as well as their relations with edaphic properties. The taxonomic diversity of bacterial communities was mainly dominated by the phyla Firmicutes, Proteobacteria and Actinobacteria. Alpha diversity was the highest in grazed pasture (OTU richness, Chao and Shannon), and it was the lowest in ungrazed pasture. Soil organic carbon, nitrogen and pH were the main determining variables of bacterial community composition and diversity. Predicted functional profiles revealed the gene abundances involved in amino acid, energy and carbohydrate metabolisms; and in categories related to nucleotide transport, metabolism, translation ribosomal structure, and biogenesis. These abundances were higher in agricultural than pastoral systems. Our results suggest that changes in soil physicochemical properties (i.e. SOC, TN and pH) associated with soil management practices cause shifts in the composition of soil bacterial communities and their metabolic functions in farming systems of the semi-arid Chaco region.

Bacterial Community Is Affected by Locations and Time Rather Than Potato Varieties but Streptomyces spp. Are Related to Potato Varieties

Improved knowledge and a better understanding of the functions of bacterial communities are vital for effective crop disease management. This study was conducted to study a bacterial community’s relationship with the common scab in four different potato varieties (Dejima, DJ; Atlantic, DS; Seohong, SH; Haryeong, HY) at two different locations (Gangneung and Chuncheon) and spatial locations (rhizosphere and furrow) at two different times (preharvest and postharvest). In addition, metagenomic sequencing was performed by extracting genomic DNA from soil samples to observe the dominant bacterial microbes and disease severity of the common scab in all the tested varieties in spatial location and time. The results suggest that the most dominant bacterial phyla in all the soil samples were Proteobacteria, Acidobacteria, and Bacteroidetes. Additionally, Streptomyces spp. were found to be more abundant in the susceptible variety (DJ) than in other varieties (DS, SH, and HY). Interestingly, bacterial communities were found to be more diverse across the two different geographical locations, spatial locations, and harvesting times, rather than the variety of potato, according to PCoA analysis. There were no interlinked changes in bacterial communities among the varieties. Moreover, the 14 most dominant bacterial genus correlation networks with Streptomyces spp. suggested that there was a significant positive and negative correlation to some extent. Alpha and beta diversity results clearly indicated that the possible reason for differences in bacterial communities might have been due to the different spatial locations, in comparison with varieties, which suggests that there was no significant correlation between bacterial community richness and diversity among the varieties.

Quorum Sensing Regulates the Hydrolytic Enzyme Production and Community Composition of Heterotrophic Bacteria in Coastal Waters.

Heterotrophic microbial communities play a central role in biogeochemical cycles in the ocean by degrading organic matter through the synthesis of extracellular hydrolytic enzymes. Their hydrolysis rates result from the community’s genomic potential and the differential expression of this genomic potential. Cell-cell communication pathways such as quorum sensing (QS) could impact both aspects and, consequently, structure marine ecosystem functioning. However, the role of QS communications in complex natural assemblages remains largely unknown. In this study, we investigated whether N-acylhomoserine lactones (AHLs), a type of QS signal, could regulate both hydrolytic activities and the bacterial community composition (BCC) of marine planktonic assemblages. To this extent, we carried out two microcosm experiments, adding five different AHLs to bacterial communities sampled in coastal waters (during early and peak bloom) and monitoring their impact on enzymatic activities and diversity over 48 h. Several specific enzymatic activities were impacted during both experiments, as early as 6 h after the AHL amendments. The BCC was also significantly impacted by the treatments after 48 h, and correlated with the expression of the hydrolytic activities, suggesting that changes in hydrolytic intensities may drive changes in BCC. Overall, our results suggest that QS communication could participate in structuring both the function and diversity of marine bacterial communities.

Bacterial community profile of the crude oil-contaminated saline soil in the Yellow River Delta Natural Reserve, China

Crude oil contamination greatly influence soil bacterial community. Proliferative microbes in the crude oil-contaminated soil are closely related to the living conditions. Oil wells in the Yellow River Delta Natural Reserve (YRDNR) region is an ideal site for investigating the bacterial community of crude oil-contaminated saline soil. In the present study, 18 soil samples were collected from the depths of 0–20 cm and 20–40 cm around the oil wells in the YRDNR. The bacterial community profile was analyzed through high-throughput sequencing to trace the oil-degrading aerobic and anaerobic bacteria. The results indicated that C15–C28 and C29–C38 were the main fractions of total petroleum hydrocarbon (TPH) in the sampled soil. These TPH fractions had a significant negative effect on bacterial biodiversity (Shannon, Simpson, and Chao1 indices), which led to the proliferation of hydrocarbon-degrading bacteria. A comprehensive analysis between the environmental factors and soil microbial community structure showed that Streptococcus, Bacillus, Sphingomonas, and Arthrobacter were the aerobic hydrocarbon-degrading bacteria; unidentified Rhodobacteraceae and Porticoccus were considered to be the possible facultative anaerobic bacteria with hydrocarbon biodegradation ability; Acidithiobacillus, SAR324 clade, and Nitrosarchaeum were predicted to be the anaerobic hydrocarbon-degrading bacteria in the sub-surface soil. Furthermore, large amount of carbon sources derived from TPH was found to cause depletion of bioavailable nitrogen in the soil. The bacteria associated with nitrogen transformation, such as Solirubrobacter, Candidatus Udaeobacter, Lysinibacillus, Bradyrhizobium, Sphingomonas, Mycobacterium, and Acidithiobacillus, were highly abundant; these bacteria may possess the ability to increase nitrogen availability in the crude oil-contaminated soil. The bacterial community functions were significantly different between the surface and the sub-surface soil, and the dissolved oxygen concentration in soil was considered to be potential influencing factor. Our results could provide useful information for the bioremediation of crude oil-contaminated saline soil.