Temporal stability of plant community productivity (‘plant community stability’ hereafter) in the face of environmental disturbance is essential for maintenance of ecosystem functioning. However, ...most existing studies that examined the biotic drivers of plant community stability concentrated on plant attributes, neglecting the potential stabilizing effects of soil microbes. Here, we conducted a 5-year field experiment to quantify plant community stability (i.e., the ratio of the temporal mean of community biomass to its standard deviation over this period) at four grassland sites with no, moderate, severe, and extreme degradation statuses in northern China. Soil bacterial communities were determined with 16S ribosomal RNA gene sequences. Our results demonstrated that high bacterial network complexity and relative abundance of oligotrophs were beneficial to improve plant community stability of moderately and severely degraded grasslands. The strong impacts of bacterial community composition on plant community stability indicated that particular taxa, especially oligotrophs and copiotrophs, determined stability. The positive relationship between bacterial network complexity and plant community stability supported the central ecological belief that complexity begets stability. Together, these findings provide a new insight into the importance of soil bacterial community composition and network complexity for buffering negative effects of grassland degradation on plant community stability.
Display omitted
•Moderate and severe degradation increased network complexity and oligotrophs.•High bacterial network complexity enhanced plant community stability.•High bacterial oligotrophic abundance promoted plant community stability.
This study conducted the sorption and biodegradation of benzoapyrene (BaP) by microbial biofilm communities developed on proxies for materials typically found in soils. The half-life of BaP was 4.7 ...and 2.3 weeks for biofilms on the inorganic carrier (BCINOR, montmorillonite) and on the organic carrier (BCOR, humic acid), respectively. In contrast, the half-life was 7.0 weeks for specialized planktonic cultures (PK). The exposure to BaP caused the development of lipid inclusion bodies inside the bacteria of the PK systems and biofilms of the BCINOR, but not on the biofilms of the BCOR system. Interestingly, the BCOR displayed not only the greatest BaP sorption capacity but also the greatest bacterial density and membrane integrity and the shortest bacteria-to-bacteria distances, which were consistent with the increased production of cell surface extracellular polymeric substances on the BCOR. Both carriers caused a noticeable shift in the bacterial genera during the biodegradation of the BaP. The BCINOR selected for Rhodococcus, Brucella, Chitinophaga, and Labrys, whereas the BCOR favored Rhodococcus and Dokdonella. It indicated that ultra-structure and BaP degradation within the organic carrier-attached biofilms differed from the inorganic ones, and suggested that the microstructural heterogeneity and microbial biodiversity from biofilms on the organic carrier promoted biodegradation.
Display omitted
•Biofilms developed on the organic carrier accelerated degradation of BaP.•Cells in biofilms on inorganic carriers formed lipid inclusions.•Biofilms formed on the organic carrier were compact, and featured more EPS.•Gammaproteobacteria and Actinobacteria were linked with the degradation of BaP.
Display omitted
•The initial bacterial community composition and diversity shaped bacterial community succession.•Variations in the PAHs types affected bacterial community composition and structure ...significantly.•Benzo (a) pyrene and benzo (a) fluoranthene posed similar effects on bacterial community.•Gram-negative bacterial community may contribute more in PAHs degradation.
Understanding the microbial community succession to polycyclic aromatic hydrocarbons (PAHs) and identification of important degrading microbial groups are crucial for the designing of appropriate bioremediation strategies. In the present study, two distinct phenanthrene enriched bacterial consortia were treated against high molecular weight (Pyrene, Benzo (a) pyrene and Benzo (a) fluoranthene) and the response was studied in term of taxonomic variations by using High Throughput Illumina sequencing and qPCR analysis. Overall, the type of PAHs significantly affected the composition and the relative abundance of bacterial communities while no obvious difference was detected between bacterial communities of benzo (a) pyrene and benzo (a) fluoranthene treatments. Genera, Novosphingobium, Pseudomonas, Flavobacterium, Mycobacterium, Hoeflae, and Algoriphagus dominated all PAHs treatment groups indicating that they could be the key PAHs degrading phylotypes. Due to the higher abundance of gram-negative PAH-ring hydroxylating dioxygenase gene than that of gram-positive bacteria in all treated groups, we speculated that gram-negative bacteria may contribute more in the PAH degradation. The studied sediments harbored rich PAHs degrading bacterial assemblages involved in both low and high molecular weight PAHs and these findings provided new insight into the perspective of microbial PAHs bioremediation in the mangrove ecosystem.
Polybrominated diphenyl ethers (PBDEs) are typical persistent organic pollutants (POPs) in the environment. However, little is known about their effects on phosphorus mineralizing bacteria (PMB) in ...eutrophic lake sediments, despite the critical role of PMB in phosphorus (P) biogeochemical cycling. In this study, we carried out a 60-day microcosm experiment to understand the effects of 2 and 20 mg kg−1 dry weight decabromodiphenyl ether (BDE-209) on the activity, abundance, diversity, and community composition of PMB in the sediment of Taihu Lake, a typical eutrophic lake in China. The results showed that BDE-209 contamination, regardless of the contamination levels, significantly increased the orthophosphate concentration in overlying water and available phosphorus concentration in sediments on day 60. Such increases may be explained by the stimulatory effects of BDE-209 on alkaline phosphatase (ALP) activity and PMB abundance. Moreover, based on Miseq sequencing of the phoD gene encoding ALP, Actinobacteria was the dominant PMB phylum in all treatments, and BDE-209 significantly increased the diversity of PMB and altered their community composition. In particular, the relative abundances of some PMB genera such as Bradyrhizobium were increased significantly after 60 days of the High treatment. A co-occurrence network analysis further revealed that the high level of BDE-209 contamination strengthened the connectivity and interspecific co-operative relationships in the PMB community. These results will help us to understand the effects of POPs on P biogeochemical cycling in eutrophic lakes and the associated microbial mechanisms.
Display omitted
•Sediment alkaline phosphatase activity was stimulated by BDE-209 contamination.•BDE-209 enhanced the abundance and diversity of phosphate mineralizing bacteria.•BDE-209 altered the community composition of phosphate mineralizing bacteria.•The interspecies co-operation of PMB community was strengthened by BDE-209.
Display omitted
•OTC was biodegradaded and electricity generation synchronously in OTC D-GM-BE MFC.•The OTC removal efficiency of O-GM-BC and O-GM-BA was 95.0% and 91.8% in eight days.•The maximum ...power density of O-D-GM-BE MFC was 2.1 times of O-C-BE MFC.•Exoelectrogens and bacteria of OTC degradation were enriched in O-GM-BA and O-GM-BC.•Mechanisms of biodegradation of OTC and EET process in D-GM-BE MFC were proposed.
A three-step method to prepare dual graphene modified bioelectrode (D-GM-BE) in microbial fuel cell (MFC) in previous studies. This study explored the biodegradation of oxytetracycline (OTC) and electricity generation in O-D-GM-BE MFC. The OTC removal efficiency of graphene modified biocathode and bioanode (O-GM-BC, O-GM-BA) was 95.0% and 91.8% in eight days. The maximum power density generated by O-D-GM-BE MFC was 86.6 ± 5.1 mW m−2, which was 2.1 times of that in OTC control bioelectrode (O-C-BE) MFC. The Rct of O-GM-BA and O-GM-BC were decreased significantly by 78.3% and 76.3%. OTC was biodegraded to monocyclic benzene compounds by bacteria. O-GM-BA was affected strongly by OTC, and Salmonella and Trabulsiella were accounted for 83.0%, while typical exoelectrogens (Geobacter) were still enriched after the maturity of biofilm. In O-GM-BC, bacteria related with OTC biodegradation (Comamonas, Ensifer, Sphingopyxis, Pseudomonas, Dechloromonas, etc.) were enriched, which contributed to the high removal efficiency of OTC.
Elevated atmospheric CO2 concentration (eCO2) may have different effects on the bacterial community with regard to C assimilation and decomposition in eutrophic waters compared to that in fresh ...waters with intermediate levels of nutrients and oceans. Aquatic plant growth under eCO2 could further modify microbial activities associated with the C cycle in eutrophic waters. Therefore, there is an urgent need to further study how eCO2 and its interactions with the growth of aquatic plants affect the composition and function of the bacterial community involved in mediating the C cycle in eutrophic waters. Accordingly, we designed a microcosm experiment to investigate the effects of ambient and high CO2 concentrations on bacterial community composition and function in eutrophic waters with and without the growth of Eichhornia crassipes (Mart.) Solms. The results from 16S rRNA gene sequencing, function prediction, and q-PCR showed that eCO2 significantly increased the abundance of bacterial and functional genes involved in CO2 assimilation (photosynthetic bacteria; cbbL IA & IC, cbbL ID, cbbM, pufM) and C decomposition (Acidimicrobiia, Thermoleophilia, Gaiellales; ChiA), illustrating the functional enrichment with photoautotrophy, hydrocarbon degradation, cellulolysis, and aromatic hydrocarbon degradation. However, eCO2 decreased the abundance of some chemoautotrophic bacteria, including nitrifying bacteria (Nitrospirae, Nitrosomonadaceae). In contrast, the cultivation of E. crassipes decreased the abundance of photosynthetic bacteria but increased the abundance of bacteria involved in complex C decomposition associated with root exudates and degradation, e.g. Fibrobacteres, Sphingobacteriales, Sphingomonadales, and Rhizobiales. eCO2 and growth of E. crassipes had opposite effects on algal density in eutrophic waters, creating interactive effects that further decreased the diversity of the bacterial community and abundance of some CO2-assimilating bacteria with nitrifying characteristics (Nitrosomonadaceae) and some C-degrading bacteria (Fibrobacteres) with denitrifying properties (Flavobacteriaceae, Sphingomonadaceae, and Gemmobacter). Therefore, the interactions between aquatic plants and the bacterial community in eutrophic waters under eCO2 would be beneficial to the environment and help alleviate the greenhouse effect.
Display omitted
•The eCO2 and plant growth had opposite impact on the CO2-assimilating bacteria.•The eCO2 and aquatic plant growth increased the abundance of C-degrading bacteria.•Interactions of eCO2 and plant decreased CO2-assimilating and C-degrading bacteria.•Growing aquatic plants under eCO2 would be benefit for alleviating greenhouse effect.
Biogas slurry, a liquid end product of animal manure fermentation, is widely used as fertilizer in crop fields. Land application may introduce antibiotics and related resistance genes from livestock ...production into agricultural soil. Nevertheless, changes in antimicrobial resistance in soil where biogas slurry has been repeatedly applied are not fully understood. In the present study, 13 veterinary antibiotics were analyzed in soils that were repeatedly sprayed with biogas slurry, and simultaneously, temporal changes in antibiotic resistance genes (ARGs) and bacterial community composition were investigated using a real-time quantitative PCR assay and MiSeq sequencing. Long-term repeated application of biogas slurry did not result in excessive accumulation of antibiotic residuals in the soil but increased the abundance of ARGs and facilitated ARG transfer among potential hosts. Although the quantitative PCR assay showed a decreasing trend for the relative abundance of ARGs over time, a relevance network analysis revealed highly complex bacteria-ARG co-occurrence after long-term application, which implied that repeated application might intensify horizontal gene transfer (HGT) of ARGs among different bacterial hosts in soil. The increased relative abundance of the intl1 gene supported the shift in ARG-bacteria co-occurrence. Furthermore, ordination analysis showed that the distributions of antibiotic resistance bacteria (ARB) and ARGs were closely related to application duration than to the influence of antibiotic residuals in the biogas slurry-treated soil environment. Additionally, natural level of ARG abundance in untreated soils indirectly suggested the presence/absence of antibiotics was not a key determinant causing the spread of antimicrobial resistance. This study provides improved insight into the effects of long-term repeated application of biogas slurry on the shift in ARG abundances and bacteria-ARG co-occurrence in soils, highlighting the need to focus on the influence of changed soil environment on the ARG transfer.
Display omitted
•Long-term repeated application of biogas slurry increases resistance risk in soils.•ARG abundance in applied soil showed a decreasing trend over time.•Various ARGs also inhabit soils without manure contamination.•ARG-bacteria co-occurrence becomes more complex over time in applied soil.•Applied duration was a key factor and mainly contributed to the transfer of ARGs.
Long-term repeated application of biogas slurry increased the relative abundance of ARGs and facilitated the horizontal transfer of ARGs among bacteria in soil.
One major goal in microbial ecology is to establish the importance of deterministic and stochastic processes for community assembly. This is relevant to explain and predict how diversity changes at ...different temporal scales. However, understanding of the relative quantitative contribution of these processes and particularly of how they may change over time is limited. Here, we assessed the importance of deterministic and stochastic processes based on the analysis of the bacterial microbiome in one alpine oligotrophic and in one subalpine mesotrophic lake, which were sampled over two consecutive years at different time scales. We found that in both lakes, homogeneous selection (i.e., a deterministic process) was the main assembly process at the annual scale and explained 66.7% of the bacterial community turnover, despite differences in diversity and temporal variability patterns between ecosystems. However, in the alpine lake, homogenizing dispersal (i.e., a stochastic process) was the most important assembly process at the short‐term (daily and weekly) sampling scale and explained 55% of the community turnover. Alpha diversity differed between lakes, and seasonal stability of the bacterial community was more evident in the oligotrophic lake than in the mesotrophic one. Our results demonstrate how important forces that govern temporal changes in bacterial communities act at different time scales. Overall, our study validates on a quantitative basis, the importance and dominance of deterministic processes in structuring bacterial communities in freshwater environments over long time scales.
Display omitted
•Putrescine and spermine were the dominant biogenic amines (BAs) in all dry sausages.•BA accumulation was closely related to their precursor free amino acids.•Staphylococcus and ...Weissella were the dominant genera in dry sausages.•Thirteen core species were significantly correlated with BAs.
This study aimed to investigate the biogenic amines (BAs) in dry sausages collected from different regions in northeast China; explore the potential correlation amongst BAs, free amino acids (FAAs) and bacterial communities; and determine the key bacteria that produced or inhibited BAs. The contents of BAs significantly differed amongst various dry sausages. The dominating BAs were putrescine and spermine. Further analysis of the FAA profile and its relationship with BAs showed that a large number of available precursor FAAs could cause the accumulation of their corresponding BAs. A total of 118 genera were identified in dry sausages amongst which Staphylococcus and Weissella were the dominant genera. From the correlation between BAs and species, 13 core species were significantly correlated with BAs; amongst them, 11 were positively correlated, and two were negatively correlated. This work assessed the levels of BAs in dry sausages from northeast China and demonstrated that available FAAs and complex bacterial composition were closely related to BA accumulation.
Knowledge of the key factors regulating soil organic carbon (OC) mineralization in response to fertilizers and lime application is essential to understanding the effects of agricultural land ...management on soil OC preservation. Microbial community composition and OC availability to microorganisms have been proposed as the two most imperative factors controlling soil OC mineralization, although their relative importance is still under debate. Here we performed a laboratory incubation in combination with high-throughput sequencing and structural equation modeling to examine the mechanisms underlying the responses of OC mineralization in the topsoil and the subsoil of a volcanic soil (an Andosol) to the additions of lime and/or phosphate. Results showed that lime and/or phosphate additions induced distinct shifts in the microbial community composition and functional profiles in the topsoil and the subsoil. We found that OC mineralization relied on microbial community composition and functionality in the topsoil but was strongly related to the quality and quantity of the water-extractable OC (indicative of the OC availability) in the subsoil. These data suggest that the key regulator controlling the response of OC mineralization to lime and/or P additions shifts from microbial community composition to OC availability as soil depth increases in the Andosol. Our findings highlight the central role of mechanisms controlling soil OC mineralization in regulating the responses of mineralization to intensive agricultural management practices.
Display omitted
•Key drivers regulating C mineralization varied at different soil depths.•Lime and P addition impact topsoil C mineralization by altering microbial properties.•Lime and P addition impact subsoil C mineralization by increasing C availability.
PDF
