Dominant Bacterial Communities Research Articles

Bacterial community analysis on Sclerotium-suppressive soil.

Difficulties in controlling the soil-borne plant pathogenic fungus Sclerotium rolfsii favoured the analysis of its suppressive soil for better understanding. In the present study, culture-independent molecular technique was used to analyse the bacterial communities of suppressive soil and conducive soil. Hence, metagenomic DNAs from both kinds of soils were directly extracted and their sequence polymorphism was analysed by targeting hypervariable domains, V4 + V5, of the 16S rRNA gene. The results of 16S rRNA gene-driven bacterial community diversity analysis along with soil physicochemical and biological properties clearly discriminated S. rolfsii suppressive soil from conducive soil. The dominant phylogenetic group of suppressive soil is Actinobacteria followed by Proteobacteria. The other groups include Acidobacteria, Firmicutes and Cyanobacteria. In contrast, conducive soil had very few Actinobacterial sequences and was dominated by Gamma- and Betaproteobacteria. Based on the relative proportion of different bacterial communities, their diversity and species richness were observed more in suppressive soil than in conducive soil. The present study identifies the dominant bacterial community which shares S. rolfsii suppressiveness.

Performance and microbial community analysis of anaerobic sludge digestion enhanced by in-situ microaeration

The effectiveness of in-situ microaeration was investigated with varied air dosages [0–25 mL/(L·d)] to enhance mesophilic anaerobic digestion (AD) of sludge in semi-continuous systems in terms of specific biogas production and volatile solids (VS) removal rate, focusing on performance evaluation, microbial community analysis, and underlying mechanisms. The optimal dosage of 12.5 mL/(L·d) increased specific biogas production by 15.8 ± 7.3% and enhanced VS removal by 18.3 ± 1.6%. In-situ microaeration stimulated activity of hydrolytic enzymes, enlarged sludge particle size, and improved sludge dewaterability. MiSeq sequencing analysis showed that dominant bacterial and archaeal communities were remarkably different between in-situ microaeration and obligate AD process. The presence of oxygen enriched relative abundances of Deltaproteobacteria, Anaerolineae, Clostridia, Synergistia and Caldilineae, enabling the acid-producing process to metabolize more types of substrates. Due to the selective enrichment, in-situ microaeration significantly enriched aceticlastic methanogens rather than hydrogenotrophic methanogens in the AD reactor. Analysis of coupling microaeration pretreatment and in-situ microaeration for anaerobic digestion indicated that excessive microaeration decreased VS removal rate and methane yield owing to substrates consumption by facultative bacteria. In-situ microaeration-based AD could be a promising process for sludge treatment and bioenergy recovery.

Effect of Active Coatings Containing Lippa citriodora Kunth. Essential Oil on Bacterial Diversity and Myofibrillar Proteins Degradation in Refrigerated Large Yellow Croaker.

The research evaluated the effects of locust bean gum (LBG) and sodium alginate (SA) active coatings containing 0.15, 0.30 or 0.60% lemon verbena (Lippa citriodora Kunth.) essential oil (LVEO) on the bacterial diversity and myofibrillar proteins (MPs) of large yellow croaker during refrigerated storage at 4 °C for 18 days. Variability in the dominant bacterial community in different samples on the 0, 9th and 18th day was observed. Pseudomonas and Shewanella were the two major genera identified during refrigerated storage. At the beginning, the richness of Pseudomonas was about 37.31% and increased for control (CK) samples during refrigerated storage, however, the LVEO-treated samples increased sharply from day 0 to the 9th day and then decreased. LBG-SA coatings containing LVEO treatments significantly delayed MPs oxidation by retarding the formation of free carbonyl compounds and maintaining higher sulfhydryl content, higher Ca2+-ATPase activity, better organized secondary (higher contents of α-helix and β-sheet) and tertiary structures during refrigerated storage. The transmission electron microscope (TEM) images showed that the integrity of the sarcomere was damaged; the boundaries of the H-, A-, and I-bands, Z-disk, and M-line were fuzzy in the CK samples at the end of storage. However, the LVEO-treated samples were still regular in appearance with distinct dark A-bands, light I-bands, and Z-disk. In brief, LBG-SA active coatings containing LVEO treatments suggested a feasible method for protecting the MPs of large yellow croaker during refrigerated storage.

The impact of environmental factors on the environmental bacterial diversity and composition in the Jiang-flavoured Baijiu production region

Moutai town is the birthplace and core producing region of Jiang-flavoured Baijiu (Moutai-flavour liquor). The unique climate conditions have made Moutai town a unique ecological environment for the production of Baijiu. We investigated the impacts of environmental factors (temperature, humidity, precipitation, sunlight and pressure) on the environmental bacterial diversity and composition across the four seasons in Moutai town. The sequenceing analysis revealed 21,424–85,577 high-quality 16S rRNA sequences were obtained from 28 environmental samples (a total of 476 samples were collected). These data indicated that the bacterial community was extremely diverse with Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria detected as the dominant environmental bacterial phyla, accounting for 99.51%. There were 8 dominant bacteria classes present amongst which Betaproteobacteria (1.83%–2.52%) and Flavobacterium (4.76%–5.74%) were for the first time identified as the dominant bacteria in Baijiu-making environments. There were 16 dominant bacterial genera (Sphingobacterium, Enterobacter, Acinetobacter, Weissella and Bacillus, etc) in the four seasons, that accounted for 54.26%. Our results also showed that the environmental bacterial community structure was relatively stable whilst bacterial diversity was related to the climate conditions. We showed that changes in environmental factors,including temperature, humidity and sunlight significantly affected bacterial diversity and composition particularly on the dominant bacterial community.

Effects of Plastic Debris on the Biofilm Bacterial Communities in Lake Water

Increasing discharge of plastic debris into aquatic ecosystems and the worsening ecological risks have received growing attention. Once released, plastic debris could serve as a new substrate for microbes in waters. The complex relationship between plastics and biofilms has aroused great interest. To confirm the hypothesis that the presence of plastic in water affects the composition of biofilm in natural state, in situ biofilm culture experiments were conducted in a lake for 40 days. The diversity of biofilm attached on natural (cobble stones (CS) and wood) and plastic substrates (Polyethylene terephthalate (PET) and Polymethyl methacrylate (PMMA)) were compared, and the community structure and composition were also analyzed. Results from high-throughput sequencing of 16S rRNA showed that the diversity and species richness of biofilm bacterial communities on natural substrate (observed species of 1353~1945, Simpson index of 0.977~0.989 and Shannon–Wiener diversity index of 7.42~8.60) were much higher than those on plastic substrates (observed species of 900~1146, Simpson index of 0.914~0.975 and Shannon–Wiener diversity index of 5.47~6.99). The NMDS analyses were used to confirm the taxonomic significance between different samples, and Anosim (p = 0.001, R = 0.892) and Adonis (p = 0.001, R = 808, F = 11.19) demonstrated that this classification was statistically rigorous. Different dominant bacterial communities were found on plastic and natural substrates. Alphaproteobacterial, Betaproteobacteria and Synechococcophycideae dominated on the plastic substrate, while Gammaproteobacteria, Phycisphaerae and Planctomycetia played the main role on the natural substrates. The bacterial community structure of the two substrates also showed significant difference which is consistent with previous studies using other polymer types. Our results shed light on the fact that plastic debris can serve as a new habitat for biofilm colonization, unlike natural substrates, pathogens and plastic-degrading microorganisms selectively attached to plastic substrates, which affected the bacterial community structure and composition in aquatic environment. This study provided a new insight into understanding the potential impacts of plastics serving as a new habitat for microbial communities in freshwater environments. Future research should focus on the potential impacts of plastic-attached biofilms in various aquatic environments and the whole life cycle of plastics (i.e., from plastic fragments to microplastics) and also microbial flock characteristics using microbial plastics in the natural environment should also be addressed.

Brassica napus phyllosphere bacterial composition changes with growth stage

AimsPhyllosphere bacteria play critical roles in plant growth promotion, disease suppression and global nutrient cycling but remain understudied.MethodsIn this project, we examined the bacterial community on the phyllosphere of eight diverse lines of Brassica napus for ten weeks in Saskatoon, Saskatchewan Canada.ResultsThe bacterial community was shaped largely by plant growth stage with distinct communities present before and after flowering. Bacterial diversity before flowering had 111 core members with high functional potential, with the peak of diversity being reached during flowering. After flowering, bacterial diversity dropped quickly and sharply to 16 members of the core community, suggesting that the plant did not support the same functional potential anymore. B. napus line had little effect on the larger community, but appeared to have more of an effect on the rare bacteria.ConclusionsOur work suggests that the dominant bacterial community is driven by plant growth stage, whereas differences in plant line seemed to affect rare bacteria. The role of these rare bacteria in plant health remains unresolved.

Gut bacterial communities across 12 Ensifera (Orthoptera) at different feeding habits and its prediction for the insect with contrasting feeding habits.

Insect microbial symbioses play a critical role in insect lifecycle, and insect gut microbiome could be influenced by many factors. Studies have shown that host diet and taxonomy have a strong influence on insect gut microbial community. In this study, we performed sequencing of V3-V4 region of 16S rRNA gene to compare the composition and diversity of 12 Ensifera from 6 provinces of China. Moreover, the influences of feeding habits and taxonomic status of insects on their gut bacterial community were evaluated, which might provide reference for further application research. The results showed that Proteobacteria (45.66%), Firmicutes (34.25%) and Cyanobacteria (7.7%) were the predominant bacterial phyla in Ensifera. Moreover, the gut bacterial community composition of samples with different feeding habits was significantly different, which was irrespective of their taxa. The highest diversity of gut bacteria was found in the omnivorous Ensifera. Furthermore, common and unique bacteria with biomarkers were found based on the dietary characteristics of the samples. However, the bacterial community structure of the Ensifera samples was significantly different from that of Caelifera. Therefore, we concluded that feeding habits and taxonomic status jointly affect the gut bacterial community composition of the samples from Orthoptera. However, the influence of feeding habit dominates when taxonomy category below the suborder level. In addition, the dominant, common and unique bacterial community structure could be used to predict the contrastic feeding habits of insects belonging to Ensifera.

Metagenomics reveals functional profiling of microbial communities in OCP contaminated sites with rapeseed oil and tartaric acid biostimulation

Organochlorine pesticides (OCPs) contaminated sites pose great threats to both human health and environmental safety. Targeted bioremediation in these regions largely depends on microbial diversity and activity. This study applied metagenomics to characterize the microbial communities and functional groups composition features during independent or simultaneous rapeseed oil and tartaric acid applications, as well as the degradation kinetics of OCPs. Results showed that: the degradation rates of α-chlordane, β-chlordane and mirex were better when (0.50% w/w) rapeseed oil and (0.05 mol L−1) tartaric acid were applied simultaneously than singular use, yielding removal rates of 56.4%, 53.9%, and 49.4%, respectively. Meanwhile, bio-stimulation facilitated microbial enzyme (catalase/superoxide dismutase/peroxidase) activity in soils significantly, promoting the growth of dominant bacterial communities. Classification at phylum level showed that the relative abundance of Proteobacteria was significantly increased (p < 0.05). Network analysis showed that bio-stimulation substantially increased the dominant bacterial community's proportion, especially Proteobacteria. The functional gene results illustrated that bio-stimulation facilitated total relative abundance of degradation genes, phosphorus, carbon, nitrogen, sulfur metabolic genes, and iron transporting genes (p < 0.05). In metabolic pathways, functional genes related to methanogenesis and ammonia generation were markedly upregulated, indicating that bio-stimulation promoted the transformation of metabolic genes, such as carbon and nitrogen. This research is conducive to exploring the microbiological response mechanisms of bio-stimulation in indigenous flora, which may provide technical support for assessing the microbial ecological remediation outcomes of bio-stimulation in OCP contaminated sites.

Contribution of bacterial extracellular polymeric substances (EPS) in surface water purification.

Naturally present aquatic microorganisms play an important role in water purification systems, such as the self-purification of surface waters. In this study, two water sources representing polluted surface water (Olympic Green; OG) and unpolluted surface water (Jingmi river; JM), were used to explore the self-purification of surface water by bacteria under different environmental conditions. The dominant bacterial community of OG and JM waters (both are Firmicutes and Proteobacteria) were isolated, cultured, and then used to carry out flocculation tests. Results showed that the flocculation ability of the dominant bacteria and extracellular polymeric substances (EPS) obtained from OG isolation was significantly greater than that from JM. Further examination illustrated that the main components of EPS were polysaccharides, which played an important role in improving the flocculation ability of bacteria. EPS from dominant cultural bacteria strains (OG1 and JM3) isolated from the two different sources lacked hydrophilic groups (e.g. COOH) and had a networked structure which are the main reasons to enhance the flocculation ability. The bacterial diversity and redundancy analysis (RDA) results also showed that microbial community composition is determined by water quality (SS, TOC, and NH4+), and different Bacteroidetes, Actinobacteria and Proteobacteria community structures can improve the water body's ability to remove environmental pollutants (such as SS, humic acid and fulvic acid). These findings provide new information showing how bacterial communities change with environmental factors while maintaining the purity of surface water.

English

The microbial activity and soil enzyme activity are closely related to soil ecological functions. In this study, a flue-cured tobacco (Nicotiana tabacum) variety, K326, was planted and subjected to tillage methods of 20 cm of rotary tillage (control, RT20), 30 cm of deep tillage (DT30), 30 cm (ST30) and 40 cm (ST40) of subsoiling tillage. The expression profiling was conducted using Illumina MiSeq high-throughput sequencing, and the changes of bacterial community structure and enzyme activity in the rhizosphere soil under different tillage treatments were assessed. In the results, the DT30, ST30 and ST40 measures significantly reduced activity of catalase, increased the activities of urease, acid phosphatase and cellulose, and increased the diversity and richness of bacterial communities in the rhizosphere soil. Compared to RT20 (control), the Shannon index of DT30 treatment increased by 3.58%, the Simpson index decreased by 47.46% and the ACE and Chao1 indexes of ST40 treatment increased by 2.77 and 3.38%, respectively. At the phylum and genus levels, the dominant bacterial communities and relative abundance of the bacterial communities under different tillage treatments were significantly different. Compared with RT20, the DT30, ST30 and ST40 treatments increased the relative abundance of Gemmatimonadetes phylum by 30.93, 20.97 and 11.44% and the relative abundance of Nitrospirae phylum increased by 54.55, 22.73 and 11.36%, respectively. In addition, the relative abundances of beneficial microorganisms such as Nocardioides, Gemmatimonas, and Sphingomonas genus in DT30 and ST30, ST40 treatments were more than control (RT20) treatments. In conclusion, the different ecological niche may create by great disturbance to soil in DT and ST treatments, the selection and adaptation of different microorganisms to the ecological niche may result in great changes in microbial species composition and community structure. © 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers © 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers© 2021 Friends Science Publishers©

Correlation between Soil Bacterial Community Structure and Soil Properties in Cultivation Sites of 13-Year-Old Wild-Simulated Ginseng (Panax ginseng C.A. Meyer)

Soil properties are one of the major factors determining the growth of vegetation. These properties drive the selection of the dominant bacterial community profiles, which eventually determines the soil quality and fertility. The abundance of preferential bacterial community assists in better productivity of a particular type of vegetation. The increasing focus on the health and well-being of the human population has resulted in a shift in paradigm to concentrate on the cultivation of medicinal plants such as Wild-simulated ginseng (WSG). These plant species take a long time for their growth and are generally cultivated in the mountainous forest trenches of Far East countries like South Korea. This study was conducted to decipher the bacterial community profiles and their correlation with soil chemical properties, which would give a broader idea about the optimum growing conditions of such an important medicinal plant. The important edaphic factor determined in this study was the soil pH, which was recorded to be acidic in all the studied cultivation sites. In agreement with the edaphic factor, the relative abundance of Acidobacteria was found to be highest as this phylum prefers to grow in acidic soils. Moreover, the total organic matter, total nitrogen and cation exchange capacity were found to be significantly correlated with the bacterial community. Hence, these results will help to identify the suitable cultivation sites for WSG and increase the productivity of these medicinal plants.

Response of bacterial community in sea cucumber Apostichopus japonicus intestine, surrounding water and sediment subjected to high-temperature stress

During the anomalously hot summer of 2018, the water temperature in a sea cucumber culture pond reached 28–33 °C. As a result, many sea cucumbers died from the high temperature, causing huge economic losses. Currently, changes in the bacterial community of the sea cucumber culture pond ecosystem during high temperature remain largely unknown. In this study, we investigated the effects of high temperature on the community composition and function of the sea cucumber culture pond ecosystem using high-throughput sequencing. The results showed that bacterial communities in the Apostichopus japonicus intestine, surrounding water and sediment responded quickly to high temperature, as indicated by an obvious succession process of the dominant and specific bacterial community. At high temperature, the richness and diversity of the bacterial community in the water and sediment decreased significantly (P < 0.05). The richness of the bacterial community in the A. japonicus intestine was significantly increased, and several potential pathogens (Staphylococcus, Vibrio and Pseudomonas) changed in terms of their dominance, increasing the risk of disease in A. japonicus. The predictive functional profiling based on the Clusters of Orthologous Groups (COGs) database showed that the restraint of water, sediment, and the intestine bacterial community under high temperature were characterized mainly by the weakening of metabolism, environmental information processing and cellular processes, and post-translational modification, protein turnover, chaperones. The bacterial community may adapt to a high temperature by enhancing information storage and processing, amino acid transport and metabolism, and carbohydrate transport and metabolism. In the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database analysis, 64 KEGG pathways showed significant differences, which could be classified into six KEGG A classes and 23 KEGG B classes. The main differences in the KEGG pathways of the bacterial community in water, sediment, and A. japonicus intestine at high temperature were reflected in metabolism, cell motility, and environmental information processing. By changing its structure and group behavior, the bacterial community might be inhibited or adapted to the high temperature with both attributes dependent on changes in functional proteins and metabolic pathways. The findings of this study provide guidance for maintaining a healthy aquaculture environment.

Fate and Risk of Florfenicol, Thiamphenicol, and Antibiotic Resistance Genes During Composting of Swine Manure

Livestock manure is considered an important source of antibiotic resistance genes (ARGs) spreading to the environment, posing a potential threat to human health. Here, we investigated the dissipation of florfenicol (FF) and thiamphenicol (TAP), and their effects on bacterial community, mobile genetic elements (MGEs), and ARGs during composting. The results indicated that FF and TAP dissipated rapidly in compost, with half-life values of 5.1 and 1.6 d, respectively. The FF and TAP residues in the manure may have a negative influence on the physicochemical factors of the compost while could reduce the elimination of ARGs and MGEs during composting. Proteobacteria and Firmicutes were the dominant bacterial communities and important potential pathogen hosts carrying ARGs. The predicted concentration of FF in soil (≥100μg/kg) indicates potential risk to the natural environment. Further studies are needed to investigate the best environmental conditions to achieve more comprehensive elimination of ARGs and MGEs during composting.

土壤微生物群落对麻栎-刺槐混交林凋落物分解的影响

以麻栎-刺槐混交林和麻栎纯林为研究对象，采用野外定点采样、室内分析与高通量测序的方法，对凋落物分解过程中土壤微生物菌群多样性特征及其对凋落物分解速率的影响进行了研究。结果表明：（1）麻栎-刺槐混交林凋落物的分解速率高于麻栎纯林。两种林分凋落物有机碳（TOC）、全氮（TN）发生释放，全磷（TP）发生积累-释放的过程。（2）两种林分土壤细菌优势类群为放线菌门（Acidobacteria）、变形菌门（Proteobacteria）、酸杆菌门（Actinobacteria）和疣微菌门（Verrucomicrobia），土壤真菌优势类群为担子菌门（Basidiomycota）、子囊菌门（Ascomycota）和被孢霉门（Moritierellomycota）。（3）凋落物分解过程中，麻栎-刺槐混交林土壤微生物菌群丰富度指数和菌群多样性指数变化范围小于麻栎纯林。（4）凋落物分解速率与土壤细菌菌群丰富度指数和菌群多样性指数呈显著正相关，与土壤真菌菌群丰富度指数呈显著正相关。土壤微生物群落对麻栎-刺槐混交林和麻栎纯林凋落物分解速率具有重要影响，研究结果为深入开展混交林土壤微生物多样性对凋落物分解的影响研究提供理论依据。;Forest ecosystems are an important part of the terrestrial ecosystem. In forest ecosystems, the plants transmit carbon, nitrogen, phosphorus and other nutrients to the soil in the form of litter. Soil microorganisms, as the main decomposers of litter, affect the energy flow and material circulation of forest ecosystems. This paper took the mixed Quercus acutissima Carruth. and Robiniapseudoacacia L. forest (QR), as well as pure Quercus acutissima Carruth forest (QAC) as research objects. The field fixed-point sampling, indoor analysis, and high-throughput sequencing methods were used to study the characteristics of soil microbial diversity and their effects on the litter decomposition rate. The results were as follows: (1) The litter decomposition rate of QR was higher than that of QAC, the litter decomposition rate of QR was 0.70, and the litter decomposition rate of QAC was 0.62. During the litter decomposition of the two forest stands (QR and QAC), total organic carbon (TOC) and total nitrogen (TN) were released, but total phosphorus (TP) was accumulated first and then released. (2) The two forest stands had the same dominant soil microbial communities, the dominant soil bacterial communities were Actiobacteria, Proteobacteria, Actinobacteria and Verrucomicrobia, and the dominant soil fungi communities were Basidiomycota, Ascomycota and Mortierierellomycota. (3) During the litter decomposition of the two forest stands, the variation range of the soil microbial community richness index and diversity index of QR was smaller than that of QAC. The bacterial community richness index (Chao1 index and ACE index) and community diversity index (Shannon index and Simpson index) of QR and QAC showed a trend of first increasing and then decreasing. The fungal community richness index of QR showed a trend of first decreasing and then increasing, and the fungal community diversity index showed a gradually decreasing trend. The fungal community richness index of QAC showed a gradually decreasing trend, and the fungal community diversity index showed a trend of first decreasing and then increasing. (4) The litter decomposition rate was significantly positively correlated with the soil bacterial community richness index and diversity index, while significantly positively correlated with the soil fungal community richness index. The soil microbial community had an important influence on the litter decomposition rate of QR and QAC. The research results are helpful to understand the relationship between the litter decomposition rate and soil microbial communities in mixed forests, and provide theoretical basis for the research of the influence of soil microbial diversity on litter decomposition in mixed forests.

Fungicides alter the distribution and diversity of bacterial and fungal communities in ginseng fields

ABSTRACT The present study was focused on comparison of four typical fungicides in ginseng field to evaluate the impact of the different fungicides on the soil bacterial and fungal communities’ composition and diversity by using high-throughput sequencing. Five treatments were designed comprising carbendazim (D), dimethyl disulfide (E), dazomet (M), calcium cyanamide (S), and control (C). The application of fungicide obviously altered the distribution of dominant fungal and bacterial communities and remarkably decreased the diversity (1099-763 and 6457-2245). The most abundant Proteobacteria obviously degenerate in fungicide-treated soil and minimum in E (0.09%) compared to control (25.72%). The relative abundance of Acidobacteria was reduced from 27.76 (C) to 7.14% after applying fungicide and minimum in E. The phylum Actinobacteria are both decomposers of organic matter and enemies of soil-borne pathogens, elevated from 11.62 to 51.54% and are high in E. The fungi community mainly distributed into Ascomycota that enriched from 66.09 to 88.21% and highin M and E (88.21 and 85.10%), and Basidiomycota reduced from 21.13 to 3.23% and low in M and E (5.27 and 3.23%). Overall, environmentally related fungicides decreased the diversity and altered the composition of bacterial and fungal communities, highest sensitivity present in dimethyl disulfide-treated soil.

Unravelling the Genetic and Function Diversity of Dominant Bacterial Communities Involved in Co-Composting Bioremediation of Complex Crude Oil Waste Sludge

The present study aimed at using metagenomic analysis for profiling the dominant endogenous bacterial diversity in a compost matrix throughout co-composting of crude oil waste sludge and animal manures using a static co-composting technique. A total of 280,666 good and filtered reads were obtained which was distributed into 17 phyla, 42 classes, 83 orders, 162 families and 359 genera. The dominant 4 phyla include Proteobacteria, Actinobacteria, Firmicutes, and Acidobacteria. At genus level both classified and unclassified, the top 12 genera’s OTUs were Sphingomonas, Pseudomonas, Burkholderia-Paraburkholderia, Microbacterium Rhodococcus, Bradyrhizobiaceae_unclassified, Sphingomonadaceae_unclassified Afipia, Methylobacterium, Bacillus, Phenylobacterium and Achromobacter. These genera have been found to be PAH-degraders because of their unique and distinct capabilities as well as vital roles they play in ex-situ and in-situ bioremediation as shown by GC/MS analysis results indicating reduction in the selected PAHs ranging from 36.52 to 99.98% over a period of 10 months of incubation and by different microbial diversity of each individual sample. With the help of metagenomics analysis, essential detailed information on the dominant bacterial diversity directly from the co-composted samples have been revealed extensively via a high-throughput Illumina sequencing application. The results indicated that the composition of the dominant bacteria community must have influenced PAH degradation. Interestingly, estimated community diversity and richness of dominant OTUs showed that co-composting of crude oil refinery waste sludge generated and harbours higher bacterial diversity as well as very important rich species for in-situ or ex-situ bioremediation. Furthermore, most OTUs for the class; Proteobacteria_unclassified, Bacteria_unclassified, Bacteroidetes_unclassified, Firmicutes_unclassified, phyla Bacteria_unclassified and genus; Bradyrhizobiaceae_unclassified, Sphingomonadaceae_unclassified, Corynebacteriales_unclassified, Enterobacteriaceae_unclassified, Rhizobiales_unclassified, Unclassified_bacteria that were identified in most of the samples have not been classified from class to genus level and this suggests that they may stand out for novel bacterial species which needs more research as well as exploration on them with regards to their capabilities in bioremediation technology.

Effects of Dietary Wheat Gluten Meal on Growth, Intestinal Morphology, and Microbiome in Juvenile Large Yellow croaker Larimichthys crocea

Wheat gluten meal (WGM) was evaluated as a replacement for fish meal (FM) for juvenile Larimichthys crocea．FM was replaced by 0%, 25%, 50%, 75%, and 100% of WGM (WGM0, WGM25, WGM50, WGM75, and WGM100, respectively). In addition, all diets except the control group were supplemented with amino acids. Fish were fed twice daily for 56 days. There were no significant differences in survival and feed conversion ratio (FCR) among all treatments (P&gt;0.05). WGM25, WGM50, and WGM75 groups had significantly higher specific growth rate (SGR) and weight gain ratio (WGR) than those fed with WGM0 (P&lt;0.05). There were no significant differences in mucosal thickness (MT), lamina propria width (LW), mucosal fold height (MH), and goblet cell quantity of single hair (GC) for all the diets (P&gt;0.05). The indexes of Chao1, Shannon, Simpson, and Good coverage in fish fed with WGM0, WGM50, and WGM100 were not significantly affected (P&gt;0.05). Firmicutes (81.03~94.03%) were the dominant bacterial community in juvenile large yellow croaker. Compared with the WGM0 group, the abundance of Firmicutes increased significantly, and Proteobacteria decreased significantly in the WGM100 group (P&lt;0.05). These results suggested that WGM could replace 366.3 g kg-1 FM of the juvenile large yellow croaker diet.

Potential ecological implication of Cladophora oligoclora decomposition: Characteristics of nutrient migration, transformation, and response of bacterial community structure

During decay, the sediment microenvironment and water quality are severely affected by excessive proliferation of harmful algae such as filamentous green algae (FGA). The frequency of this FGA is increased through global warming and water eutrophication. In the present study, the degradation processes of a common advantage FGA Cladophora oligoclora and its effect on nitrogen and phosphorus nutrient structure and bacterial community composition at the sediment-water interface were investigated by stable isotope labelling and high-throughput sequencing. The results showed that the decomposition process of C. oligoclona was fast, stable, and difficult to degrade. The changes in sediment δ15N values reached 66.68 ‰ on day 40, which indicated that some of the nitrogen had migrated to the sediment from C. oligoclona litter. TN and NH4+-N in the overlying water rapidly increased between days 0–10, NH4+-N rose to 78.21% of TN on day 40, resulting in severe pollution of ammonia in the overlying water. The nitrogen forms and contents in the sediment are mainly derived from the increasing ammonia nitrogen release. The TP and IP in the overlying water increased to the highest concentrations of 6.68±0.64, 6.59±0.79 mg·L−1 during the decomposition process, respectively, resulting in the migration of phosphate to the sediments with increasing phosphorus content. The abundance of the main dominant bacterial communities, such as Acinetobacter (0.08%–62.48%) and Pseudomonas (0.13%–20.36%) in sediments and overlying water has changed significantly. The correlation analysis results suggested that the phosphorus was mainly related to the bacterial community in the overlying water, while the various forms of nitrogen demonstrated a high relevance with the bacterial community in the sediment. Our research results will be valuable in evaluating the potential ecological risk of FGA decomposition and provide scientific support for shallow lake management and submerged vegetation restoration.

Can biochar regulate the fate of heavy metals (Cu and Zn) resistant bacteria community during the poultry manure composting?

In this study, the influence of coconut shell biochar addition (CSB) on heavy metals (Cu and Zn) resistance bacterial fate and there correlation with physicochemical parameters were evaluated during poultry manure composting. High-throughput sequencing was carried out on five treatments, namely T1−T5, where T2 to T5 were supplemented with 2.5%, 5%, 7.5% and 10% CSB, while T1 was used as control for the comparison. The results of HMRB indicated that the relative abundance of major potential bacterial host altered were Firmicutes (52.88–14.32%), Actinobacteria (35.20–4.99%), Bacteroidetes (0.05–15.07%) and Proteobacteria (0.01–20.28%) with elevated biochar concentration (0%−10%). Beta and alpha diversity as well as network analysis illustrated composting micro-environmental ecology with exogenous additive biochar to remarkably affect the dominant resistant bacterial community distribution by adjusting the interacting between driving environmental parameters with potential host bacterial in composting. Ultimately, the amendment of 7.5% CSB into poultry manure composting was able to significantly reduce the HMRB abundance, improve the composting efficiency and end product quality.

Bacteria are more sensitive than fungi to moisture in eroded soil by natural grass vegetation restoration on the Loess Plateau

Community composition and respiration rates of bacterial and fungal communities from grass-covered eroded soils of the Loess Plateau responded differently to constant and increasing soil moisture (SM) regimes. The soils were incubated with SM contents of 5%, 30%, and 45% and with wetting processes in the SM ranges from 5% to 30% (5–30%), from 5% to 30% to 45% (5–30–45%) and from 30% to 45% (30–45%); high-throughput sequencing and co-occurrence network analyses were applied to investigate the different responses of the bacterial and fungal communities to changed SM. Our results showed that bacteria were more sensitive than fungi to changes in SM. The dominant bacterial communities converted from Actinobacterial to Proteobacteria and Acidobacteria in 5–30–45% wetting procedure. Firmicutes preferred wet condition and exhibited slow resilience. However, no difference was observed for the Chloroflexi communities across any sample. The obvious difference in fungal composition was found between the wetting process of 5–30–45% and constant 45% SM. During the 5–30–45% procedure, the respiration rate was higher than that at 30–45% procedure after incubation for 24 days. The respiration rate in 5–30% procedure was lower than that of 5–30–45% process after incubation for 16–27 days. The larger effects on bacterial response than on fungi were verified in network analysis. Multiple stepwise regression analysis showed that 84.40% of the variation in bacterial richness and diversity as well as fungal diversity can be explained by changes in soil respiration rate in response to wetting procedure. Understanding the response of difference between bacterial and fungal community composition, phylum-levels networks and respiration rate to changes in SM is essential for the management of plant-soil-water relationship in the ecosystem after natural vegetation restoration on the Loess Plateau.