Functional Diversity Of Bacterial Communities Research Articles

The Effect of Biofumigation on the Microbiome Composition in Replanted Soil in a Fruit Tree Nursery

The imbalance of the soil microbiome is a primary indicator of ARD (apple replant disease). Biofumigation is a treatment that enables the restoration of microbiome balance. This study involved an analysis of the taxonomic and functional diversity of bacterial communities in replanted soil (ARD), in replanted soils with forecrops of French marigold (Tagetes patula L.), white mustard (Sinapis alba), and oilseed radish (Raphanus sativus var. oleifera), and in agricultural soil. The biofumigation treatment with phytosanitary plants changed the structure and abundance of the replanted soil microbiome in a fruit tree nursery. The count of operational taxonomic units (OTU) of the Proteobacteria, Bacteroidota, Patescibacteria, Chloroflexi, and Verrucomicrobiota phyla increased, whereas the count of the Firmicutes, Acidobacteriota, and Actinobacteriota phyla decreased. Biofumigation caused an increase in the content of some dominant bacterial genera, such as Flavobacterium, Massila, Sphingomonas, Arenimonas, and Devosia, in the replanted soil. Their presence in the soil may improve the growth of plants, induce their systemic resistance, and thus improve the production properties of soil with ARD. The research results led to the conclusion that the use of phytosanitary plants in nursery production can be an effective alternative to the chemical fumigation of soil.

Composition and functional diversity of bacterial communities during swine carcass decomposition.

This study investigated the changes in bacterial communities within decomposing swine microcosms, comparing soil with or without intact microbial communities, and under aerobic and anaerobic conditions. The experimental microcosms consisted of four conditions: UA, unsterilized soil-aerobic condition; SA, sterilized soil-aerobic condition; UAn, unsterilized soil-anaerobic condition; and San, sterilized soil-anaerobic condition. The microcosms were prepared by mixing 112.5 g of soil and 37.5 g of ground carcass, which were then placed in sterile containers. The carcass-soil mixture was sampled at day 0, 5, 10, 30, and 60 of decomposition, and the bacterial communities that formed during carcass decomposition were assessed using Illumina MiSeq sequencing of the 16S rRNA gene. A total of 1,687 amplicon sequence variants representing 22 phyla and 805 genera were identified in the microcosms. The Chao1 and Shannon diversity indices varied in between microcosms at each period (p<0.05). Metagenomic analysis showed variation in the taxa composition across the burial microcosms during decomposition, with Firmicutes being the dominant phylum, followed by Proteobacteria. At the genus level, Bacillus and Clostridium were the main genera within Firmicutes. Functional prediction revealed that the most abundant Kyoto encyclopedia of genes and genomes metabolic functions were carbohydrate and amino acid metabolisms. This study demonstrated a higher bacteria diversity in UA and UAn microcosms than in SA and SAn microcosms. In addition, the taxonomic composition of the microbial community also exhibited changes, highlighting the impact of soil sterilization and oxygen on carcass decomposition. Furthermore, this study provided insights into the microbial communities associated with decomposing swine carcasses in microcosm.

Taxonomic and functional diversity of bacterial communities of agriculture soil exposed to zinc peroxide nanoparticles (nZnO2)

Zinc peroxide nanoparticles (nZnO2) have interesting physicochemical properties for multiple industrial applications. Due to their wide use, their direct or indirect release and accumulation in soil represent a potential risk for microbial communities, among others. However, no reports have been found on their potential ecological risks in their soil-fate environment. Thus, this study evaluates the effect of nZnO2 on taxonomic and functional diversity of bacterial communities (BC) of agriculture soil. For this purpose, the soil was exposed to three concentrations of nZnO2 (10, 100 and 1000 mg/kg of soil) in microcosms that were evaluated after 15 and 30 days. The taxonomic and functional diversity of the BC was determined using amplicon sequencing (16S rRNA), physiological profiles (CLPP) and enzymatic activity. Exposure to low concentrations of nZnO2 (up to 100 mg/kg soil) on days 15 and 30 led to an increase of taxonomic diversity, while at 1000 mg/kg nZnO2, taxonomic and functional diversity were reduced in both exposure times. At day 30 (1000 mg/kg nZnO2), a significant impact on taxonomic diversity was manifested by (i) reduction in relative abundance of approximately 40 taxonomic groups, mainly from Rhizobiales, Azospirillales (Pseudomonadota, synonym: Proteobacteria) and increase in relative abundance of Lachnospirales (Bacillota, synonym: Firmicutes), Bacteroidales (Bacteroidota, synomym: Bacteroidetes) and others; (ii) reduction in metabolism of amino acids and amines/amides; and (iii) increase in dehydrogenase and urease activities with respect to the controls. These findings may indicate that the accumulation of large concentrations of nZnO2 in soil would negatively affect the soil biological functions, due to changes in the taxonomic and functional diversity of its BC, whereas low concentrations would likely promote them.

Effect of phenol formaldehyde-associated microplastics on soil microbial community, assembly, and functioning.

Increasing investigations explore the effects of plastic pollutants on bacterial communities, diversity, and functioning in various ecosystems. However, the impact of microplastics (MPs) on the eukaryotic community, microbial assemblages, and interactions is still limited. Here, we investigated bacterial and micro-eukaryotic communities and functioning in soils with different concentrations of phenol formaldehyde-associated MPs (PF-MPs), and revealed the factors, such as soil properties, microbial community assembly, and interactions between microbes, influencing them. Our results showed that a high concentration (1%) of PF-MPs decreased the microbial interactions and the contribution of deterministic processes to the community assembly of microbes, and consequently changed the communities of bacteria, but not eukaryotes. A significant and negative relationship was determined between N2O emission rate and functional genes related to nitrification, indicating that the competitive interactions between functional microbes would affect the nitrogen cycling of soil ecosystem. We further found that vegetable biomass weakly decreased in treatments with a higher concentration of PF-MPs and positively related to the diversity of micro-eukaryotic communities and functional diversity of bacterial communities. These results suggest that a high concentration of the PF-MPs would influence crop growth by changing microbial communities, interactions, and eukaryotic and functional diversity. Our findings provide important evidence for agriculture management of phenol formaldehyde and suggest that we must consider their threats to microbial community compositions, diversity, and assemblage in soils due to the accumulation of PF-MPs widely used in the field.

How Important Are the Relations between Vegetation Diversity and Bacterial Functional Diversity for the Functioning of Novel Ecosystems?

Understanding ecosystem development of post-mining areas requires observing the development of the plant and microbial communities. It is widely known that mutual interaction is important for both of these groups, and both benefit significantly. The aim of this study was to broaden the knowledge about the relation between the vegetation and functional diversity of bacterial communities in novel ecosystems of post-mining areas and to discuss the potential applicability of methods of studies of bacterial functional diversity in these ecosystems with special attention paid to the BIOLOG method. The functional diversity of microbial communities of five types of microhabitats of post-coal mining heap (Upper Silesia, Poland) was studied using the BIOLOG method. Four of them were covered by spontaneously developed vegetation (two dominated by grasses Calamagrostis epigejos and Poa compressa and two others by dicotyledonous species Daucus carota and Tussilago farfara). The results obtained for vegetated microhabitats were compared with the diversity of microbial communities from non-vegetated types of microhabitat. Our study confirmed that microbial functional diversity measured by the summed area under the curve for all substrates, the richness index, the Shannon-Wiener index and the evenness index mirrors aboveground vegetation diversity. All of these measures differ, especially between non-vegetated patches and grassland patches dominated by C. epigejos and P. compressa.

A 16S rRNA amplicon approach to the structural and functional diversity of bacterial communities associated with horse gram crop for drought mitigation and sustainable productivity.

In this study, 16S rRNA amplicon sequencing analyses were performed to determine the diversity of the bacterial community present in the soil, rhizosphere region, root nodules and seeds of the horse gram plant. We observed the dominance of Proteobacteria, Actinobacteria, Firmicutes, Acidobacteria, Bacteroidetes, Planctomycetes and Gemmatimonadetes across all four domains of the horse gram plant. For community analyses, the significance of the alpha diversity was estimated using the Shannon index, Simpson index and Chao1 index, which revealed no significant difference among the samples. However, the estimation of the beta diversity indicated a significant difference among the samples, with p < 0.001 and R2 =1. A strong positive correlation was found between the rhizosphere and root nodule samples. Comparative genomics of the 16S rRNA gene showed that ammonium-oxidizing metabolism (amoA), nitrite-reducing metabolism (nirK) and nitrogen-fixing metabolism (nifH) were prominent mechanisms in all samples. The genes involved in the biosynthesis of amino acids, purine metabolism and nitrogen metabolism were identified as the key genes associated with the functional traits of microbial domains in horse gram. The culturable microbes associated with horse gram can be used as a substitute for synthetic fertilizers to maintain soil fertility and ecological health in agricultural practices. Determining the survival strategies of bacterial communities that positively respond to multiple gate selection helps in understanding the structural diversity and functional traits primarily focused on the development of beneficial microbial consortium for promoting plant growth.

Insight into the Taxonomic and Functional Diversity of Bacterial Communities Inhabiting Blueberries in Portugal.

Vaccinium myrtillus is a dwarf shrub of the Ericaceae family with a Palearctic distribution, associated with temperate and cold humid climates. It is widespread on the European continent; on the Iberian Peninsula it is located on Atlantic climate mountains and glacial relicts. In Portugal, we find scattered and interesting populations; however, the majority of them are threatened by climate change and wildfires. Given that, the objective of this study is to determine the rhizospheric and root bacterial communities of this plant in the southernmost regions, and, consequently, its potential range and ability to be used as a biofertilizer. In this work, metabarcoding of 16S rRNA gene showed that the endophytic bacterial diversity is dependent on the plant and selected by it according to the observed alpha and beta diversity. Moreover, a culturomic approach allowed 142 different strains to be isolated, some of them being putative new species. Additionally, some strains belonging to the genera Bacillus, Paenibacillus, Pseudomonas, Paraburkholderia, and Caballeronia showed significant potential to be applied as multifunctional biofertilizers since they present good plant growth-promoting (PGP) mechanisms, high colonization capacities, and an increase in vegetative parameters in blueberry and tomato plants.

Insights into the spatio-temporal composition, diversity and function of bacterial communities in seawater from a typical laver farm

Laver is the most widely farmed seaweed with the largest culture area in China. The spatio-temporal variations in composition, diversity, and functional properties of bacteria in seawater as well as the environmental variables of seawater in a large-scale laver farm in China were studied. Both the community richness indices and Shannon index in the laver farming area remained at a relatively stable level during laver cultivation. Fifty-nine prokaryotic phyla were detected in all samples, however, only six of these phyla accounted for 98.84% of all sequences. Proteobacteria, Gammaproteobacteria, Rhodobacterales, Rhodobacteraceae, and Octadecabacter were the most predominant bacterial taxa at different levels of classification. The keystone bacterial taxa were Bacteroidetes, Pseudomonadales, Rhodobacterales, Flavobacteriales, Loktanella, and Pseudoruegeria based on network analysis. Members of representative bacterial biomarker taxa in November may be associated with degradation of algal cell wall polysaccharides. A significant increase in metabolic exchange and transformation nutrients occurred in the seawater during the early and late stage of laver cultivation, indicating that the laver reproductive activities (i.e. the formation/release activities of archeospores and zygotospores) probably drove the variation of metabolic functional diversity of bacterial communities. Based on Mantel test and redundancy analysis, we found the hydrographic parameters (e.g. salinity, temperature, DO, pH) as well as the key carbon (e.g. POC, DOC) and nitrogen parameters (e.g. nitrate, DIN, DON, TDN) were crucial environmental variables to shape the bacterial community composition in the surrounding seawater of laver farm. In a word, our results suggested that the microbial community structure and function significantly changed across the different succession stages during laver cultivation. This work provides new insights on the characteristics of bacterial communities in a large-scale laver farming system and solidifies the importance of laver farming in shaping seawater microbiomes.

Retraction: Metagenomic analysis exploring taxonomic and functional diversity of bacterial communities of a Himalayan urban fresh water lake.

Retraction: Metagenomic analysis exploring taxonomic and functional diversity of bacterial communities of a Himalayan urban fresh water lake.

Cross-biome metagenomic analyses of the impact of pollutants on taxonomic and functional diversity of bacterial communities from different geographical regions

Due to anthropogenic activities, a large number of pollutants are disposed into the environment. The microbial communities in the environment are immensely diverse and critical mediators of various ecosystem processes. But it is not clearly known to what extent xenobiotics effect the composition and functionality of environmental microorganisms, across biomes in different geographic locations, with varying contaminating sources, categories of chemical pollutants, and their application types. Here, we investigated the impact of xenobiotics by metagenomic analysis of 16S rRNA from seawater, soil, sludge and sediment, for deciphering microbial diversity, community structure, functional enrichment and metabolic potentiality in relation to the application of pesticide (metaldehyde), herbicide (2,4-dichlorophenoxyacetic acid; DCPAA), insecticide (chlordecone) and flame retardant additives (organophosphate triesters; OPT and tris 2 chloroethyl phosphate; TCEP). Firmicutes was the most abundant phylum consisting of Clostridia, in association with DCPAA (Lutispora sp.), metaldehyde and TCEP treatments. The next two abundant phyla were Proteobacteria [class Deltaproteobacteria, Alphaproteobacteria (Pelagibacter ubique with OPT treatment) and Gammaproteobacteria], and Euryarchaeota consisting mostly of Methanobacteria with chlordecone and DCPAA. Both Desulfomicrobium and Sedimentibacter were predominant in the subtropical moist forest sediment, while Synechococcus and Pelagibacter dominated the temperate Mediterranean Sea. Ruminococcus and Lutispora were more abundant in rain forest compared to waste water solid, while Anaerovorax predominated subtropical moist forest. Sequences involved in house-keeping genes comprised the most abundant hits. The genes involved in environmental information processing such as ABC transporters catalyzing carbohydrate uptake, membrane transport and quorum sensing were over-represented with TCEP, DCPAA, OPT and metaldehyde. Exposure to different classes of xenobiotics revealed major differences in microbial structure and function abundances, mainly driven by environmental sources and biomes. Preponderance of core metabolic functional genes across all the metagenomes analysed is indicative of microbial community responding and adjusting itself to deal with these treatments and maintain its balance.

Functional diversity of bacterial communities in the rhizosphere of maize grown on a soil under organic and inorganic fertilization

Accurate knowledge of bacterial metabolic processes is essential for comprehending and manipulating the agroecosystem for proper nutrients management and crop production. In this study, we focused on evaluating the functional diversity of bacterial communities associated with the rhizosphere of maize treated with organic and inorganic fertilizers. Soil samples were collected from the maize rhizosphere and sequenced using Illumina NovaSeq technology. The samples were analyzed for functional potential using the MG-RAST online tool. Our result showed that the metabolic functions differed between the clusters of group 1 - compost 8 t ha−1, 60 kg ha−1, and control (Cp8, N1, and Cn0) and group 2–120 kg ha−1 and 4 t ha−1 (N2 and Cp4) based on the similarities of fertilizers effects on the metabolic functions of the soil bacterial communities. At the genus level, Capnocytophaga and Porphyromonas were dominant in the Cp4 (4 t ha−1 compost manure) samples, Actinoplanes, Saccharomonospora, and Thermobifida were predominant in Cp8 (8 t ha−1 compost manure) treated soil. Bacillus and Granulicatella were most abundant in soil treated with high levels inorganic fertilizers (N2–120 kg ha−1). And N1 (60 kg ha−1 inorganic fertilizer) treated soil supported bacteria belonging to Norcardiodes and Mycobacterium, while Arthrobacter, Micromonospora, and Xanthomonas were predominant in the control sample (Cn0). To maintain a viable and metabolically functional bacterial community in the soil, application of a high quantity of compost (8 t ha−1) or a small quantity of inorganic fertilizer (60 kg ha−1) is suitable.

Structure and Functional Diversity of Bacterial Community in Rhizosphere Soil of Typical Vegetation in the Riparian Zone Along the Downstream of Songhua River

The aim of this study was to provide a reference for the riparian zone with protection and ecological restoration by analyzing the differences in typical vegetation (Phragmites communis, Populus tomentosa, Salix sungkianica, and Carex schmidtii) rhizosphere bacterial communities and their functions and identifying the potential of different types of vegetation to restore the damaged riparian zone in Songhua River. The 16S rRNA of rhizosphere soil bacteria in the four typical vegetation types of the riparian zone along the downstream of the Songhua River was sequenced using the Illumina MiSeq PE300 high-throughput sequencing platform. The community diversity, functional differences, and influencing factors of rhizosphere soil bacteria for different vegetation types were analyzed. The results showed that the Ace index, Chao1 index, and Shannon index of soil bacterial diversity in P.communis were significantly higher than those of P.tomentosa (P<0.05), and there was no significant difference between the above two types of vegetation and S. sungkianica and C.schmidtii. There were significant differences between the soil bacterial community structure of P. tomentosa and that of the three other vegetation types (P<0.05). The soil bacterial community structures of S.sungkianica, C.schmidtii, and P.communis were similar. Bacteria in the rhizosphere soil of the four typical vegetation types could be divided into 38 phyla. Acidobacteria, Actinobacteria, Chloroflexi, Verrucomicrobia, and Proteobacteria were the dominant phyla (relative abundance>5%), and the Nitrospirae, Gemmatimonadetes, Bacteroidetes, Firmicutes, and Rokubacteria of bacteria had a relative abundance greater than 1%. The bacterial community in the rhizosphere soil of the four typical vegetation types had 6 primary metabolic pathways and 43 secondary metabolic pathways, including 14 types of main secondary metabolic pathways (relative abundance>1%). Diversity in rhizosphere soil bacterial communities of different vegetation types was significantly influenced by the C/N ratio, soil pH, and moisture content. Hence, the effects of different vegetation types in repairing the degraded riparian zone were different, and wetland vegetation (S.sungkianica and C.schmidtii) was conducive to the improvement in soil bacterial diversity and soil ecosystem functions.

Effects of Nutrient Levels and Rice Cultivation on Taxonomic and Functional Diversity of Bacterial Communities in Flooded Soils of the Hanon Maar Crater, Korea

Agricultural land use may deteriorate soil bacterial diversity and function in an agroecosystem. This study aimed to explore the impact of agricultural disturbance on the taxonomic and functional diversity of soil bacteria using a high-throughput sequencing method. We examined the bacterial community diversity in five types of flooded soils in the Hanon Maar Crater from two types of canals characterized by different nutrient levels and three field types with a different rice cultivation history. Proteobacteria (43.2%), Chloroflexi (19.8%), Acidobacteria (15.8%), Actinobacteria (5.1%), and Nitrospirae (5.0%) were the dominant phyla (&gt;5%). The relative abundance of Actinobacteria was 7.1 times greater in the abandoned fields than in the polluted canal. Alpha diversity indices of taxonomic diversity showed strong negative correlations with C, N, and NH4+ levels. The 1.7-fold greater number of operational taxonomic units (OTUs) in abandoned fields than in paddy fields may be caused by factors other than nutrients. Functional analysis revealed that 11 putative functions, including cellulolysis and ligninolysis, were significantly affected by soil management. Functional diversity indices showed negative correlations with electrical conductivity (EC) and NH4+. Nitrogen input had a greater effect on bacterial taxonomic diversity than on functional diversity. Available P was positively correlated with the diversity indices. Taken together, these results suggest that keeping land fallow for more than 5 years and monitoring of C, N, and P levels are practical approaches for restoring taxonomic diversity but not functional diversity of soil bacteria. Our study demonstrated a decoupled response of taxonomic and functional diversity to rice cultivation, highlighting the necessity of further studies on the impact of decoupling on the stability of ecosystem functioning.

Effects of Environmental and Spatial Variables on Bacteria in Zhanjiang Mangrove Sediments.

The bottom mud of mangroves contains numerous microbial groups that play an important role in the main ecological functions of the mangrove ecosystem. The diversity and functional and environmental factors related to microbial communities, in terms of the assembly process and in environmental adaptation of the abundance and rare bacterial communities in the mangrove ecosystem, have not been fully explored. We used 16S high-throughput sequencing and operational taxonomic unit analysis to compare the diversity and composition of bacterial communities in different tidal zones in the sediments of the Zhanjiang Gaoqiao Mangrove Nature Reserve, compare the ecological adaptation thresholds and phylogenetic signals of bacterial communities under different environmental gradients, and examine the factors affecting the composition of the bacterial community. The diversity of microbial species and structure and function of the mangrove sediments were affected by the environment, showing the trend: mid tide zone > climax zone > low tide zone. Organic matter content, oxygen content, pH, and total phosphorus were identified as important environmental factors determining the functional diversity of bacterial communities and survival, while pH influences species evolution. The abundant taxa showed a wider response threshold and stronger phylogenetic signals of ecological preference across environmental gradients compared to rare taxa. The abundant bacterial groups have broader environmental adaptability than rare bacterial groups, and different environmental factors affect different communities and functions in the mangrove ecological environment. These results elucidate the mechanism underlying the generation and maintenance of bacterial diversity in response to global environmental changes.

Successional patterns of bacterial communities and their functions in shrimp aquaculture pond water across farming phases

Microorganisms, as integral components of food webs, play key roles in regulating the aquatic environment in shrimp farming. However, the abundance and functional diversity of bacteria in shrimp aquaculture ponds and the factors shaping their distribution patterns remain largely unknown. We investigated the temporal and depth changes of the bacterial communities in water columns of shrimp ponds in the Min River estuary, southeastern China. Proteobacteria was the most dominant phylum throughout the aquaculture period. The differences in the pattern of variation in bacterial communities among three water column depths were minimal. As a potential pathogen, the genus Vibrio gradually increased in relative abundance from the initial to the final farming phase. Network analysis indicated that the degrees of species segregation were higher, and the average path lengths shorter, during the middle and final farming phases compared with the initial farming phase. This suggested that environmental stimuli are more efficient at reaching the whole network and are potentially more susceptible to external disturbance during the latter two phases. Anaerobic bacteria were most abundant during the middle and final farming phases. Salinity and chlorophyll a concentration were the variables most strongly correlated with the bacterial communities during all phases, and abiotic selection accounted for most of the total variation during the three farming phases. These findings contribute to a deeper understanding of the temporal changes in the composition and functional diversity of bacterial communities in coastal shrimp pond water columns and have implications for the effective and sustainable management of shrimp aquaculture systems.

Metagenomic analysis exploring taxonomic and functional diversity of bacterial communities of a Himalayan urban fresh water lake.

Freshwater lakes present an ecological border between humans and a variety of host organisms. The present study was designed to evaluate the microbiota composition and distribution in Dal Lake at Srinagar, India. The non-chimeric sequence reads were classified taxonomically into 49 phyla, 114 classes, 185 orders, 244 families and 384 genera. Proteobacteria was found to be the most abundant bacterial phylum in all the four samples. The highest number of observed species was found to be 3097 in sample taken from least populated area during summer (LPS) whereas the summer sample from highly populated area (HPS) was found most diverse among all as indicated by taxonomic diversity analysis. The QIIME output files were used for PICRUSt analysis to assign functional attributes. The samples exhibited a significant difference in their microbial community composition and structure. Comparative analysis of functional pathways indicated that the anthropogenic activities in populated areas and higher summer temperature, both decrease functional potential of the Lake microbiota. This is probably the first study to demonstrate the comparative taxonomic diversity and functional composition of an urban freshwater lake amid its highly populated and least populated areas during two extreme seasons (winter and summer).

Uncovering multi-faceted taxonomic and functional diversity of soil bacteriomes in tropical Southeast Asian countries

Environmental microbiomes encompass massive biodiversity and genetic information with a wide-ranging potential for industrial and agricultural applications. Knowledge of the relationship between microbiomes and environmental factors is crucial for translating that information into practical uses. In this study, the integrated data of Southeast Asian soil bacteriomes were used as models to assess the variation in taxonomic and functional diversity of bacterial communities. Our results demonstrated that there were differences in soil bacteriomes across different geographic locality with different soil characteristics: soil class and pH level. Such differences were observed in taxonomic diversity, interspecific association patterns, and functional diversity of soil bacteriomes. The bacterial-mediated biogeochemical cycles of nitrogen, sulfur, carbon, and phosphorus illustrated the functional relationship of soil bacteriome and soil characteristics, as well as an influence from bacterial interspecific interaction. The insights from this study reveal the importance of microbiome data integration for future microbiome research.

Acetobacter orientalis XJC-C with a high lignocellulosic biomass-degrading ability improves significantly composting efficiency of banana residues by increasing metabolic activity and functional diversity of bacterial community

Banana residues are an important energy resource after fruit harvesting. The optionally dumping and burning causes severely environmental problems. Traditional compost efficiency was limited by lignocellulosic composition of banana residues. Inoculation with cellulase-producing microbes provides an efficient strategy for improving degradation of lignocellulosic materials. In our study, a newly isolated cellulolytic bacterium Acetobacter orientalis XJC-C with a salt and high temperature resistance was identified from a marine soft coral. By contrast, the strain can biodegrade different lignocellulosic agricultural residues, especially banana straw. The highest cellulolytic and ligninolytic enzyme activities were detected during composting at 40 days. Compared with the negative and positive control groups, the lignin degradation rate reached 76.24% in the A. orientalis XJC-C group, increased by 47.08% and 21.85%, respectively. Moreover, the strain improved significantly the metabolic activity and functional diversity of bacterial community. Hence, A. orientalis XJC-C will be a promising candidate for degrading lignocellulosic agricultural residues.

High Taxonomic and Functional Diversity of Bacterial Communities Associated with Melon Fly, Zeugodacus cucurbitae (Diptera: Tephritidae).

The next generation sequencing (NGS) approach has facilitated the investigations of gut microbiota with high throughput and resolution. The present study was focused on the taxonomic and functional characterization of bacterial community associated with different developmental stages of melon fly, Zeugodacus cucurbitae using 16S ribosomal RNA (rRNA) gene amplicons metagenomics. Z. cucurbitae is considered an invasive and most staid polyphagous pest of cucurbitaceous and other related crops. The taxonomic analysis of highly variable V3-V4 region of bacterial 16S rRNA gene sequencing indicated that the bacterial community associated with Z. cucurbitae consists of a total of 23 bacterial phyla (including unclassified and unassigned bacteria), comprising 32 classes, 69 orders, 99 families and 130 genera. Proteobacteria, Firmicutes, Actinobacteria and Tenericutes were dominant phyla of which family, Enterobacteriaceae was the most abundant in the larval and adult female stages, whereas Mycoplasmataceae was the dominant in the pupal stage. In larval stages of Z. cucurbitae, genus Providencia and Comamonas were the most abundant. However, genus Candidatus-Bacilloplasma and Klebsiella werethe most dominant in pupae and adult females of Z. cucurbitae, respectively. PICRUSt analysis conducted for prediction of metabolic activities revealed that associated microbiota were involved in membrane transport, carbohydrate metabolism, amino acid metabolism, energy metabolism, replication and repair processes as well as cellular processes and signalling. The higher number of OTUs was annotated for phosphoglycerate mutase and transketolase in adult females followed by larval stages, which may support the digestive function of the microbiota in larvae and adult females. Our findings provide insights about the high variation in microbiota across developmental stages and basis for microbiota-based management strategies of fruit flies.

Spatial distribution and influencing factors on the variation of bacterial communities in an urban river sediment.

The water and sediments of urban rivers are spatially heterogeneous because of the influence of environmental and anthropogenic factors. However, the spatial and functional diversity of bacterial communities in urban river sediments are unclear. We investigated the spatial distribution of microbial compositions in sediments in Qingdao section of the Dagu River, and the effects of sediment physiochemical properties on the variation were explored. Among the seven heavy metals analyzed, only the average concentration of Cd significantly exceeded the safety limit for sediments. The detailed composition and spatial distribution of bacterial communities fluctuated substantially between sites along the river. Bacterial datasets were separated into three clusters according to the environmental characteristics of sampling areas (the urbanized, scenic, and intertidal zones). For the urbanized zone, Acidobacteria, Firmicutes, Gemmatimonadetes, Bacteroidetes, and Gammaproteobacteria were significantly enriched, implying the effects of human activity. In the intertidal zone, Alphaproteobacteria and Deltaproteobacteria were significantly enriched, which are associated with S redox processes, as in the marine environment. Variation partitioning analysis showed that the amount of variation independently explained by variables of Na, Al, total S and Zn was largest, followed by sediment nutrients, while heavy metals and pH explained independently 13% and 9% of the variance, respectively. Overall, microbial structures in the Dagu River exhibited spatial variation and functional diversity as a result of natural and anthropogenic factors. The results will enable the prediction of the changes in urban river ecosystems that maintain their ecological balance and health.