Structure of the epiphytic bacterial communities of Macrocystis pyrifera in localities with contrasting nitrogen concentrations and temperature

沉水植物叶表附着大量细菌,与沉水植物构成了复杂的共生体系.叶片附着细菌是水生态的重要组成部分,能影响沉水植物自身生长和水体物质循环过程.目前,对于沉水植物多样性对植物叶片附着细菌群落的影响知之甚少.本研究比较了不同沉水植物物种多样性对浮游细菌和叶片附着细菌群落的影响,同时探究不同植物——苦草(Vallisneria natans)、穗状狐尾藻(Myriophyllum spicatum)、微齿眼子菜(Potamogeton maackianus)和黑藻(Hydrilla verticillata)叶片附着细菌的群落结构和多样性特征.结果表明,浮游细菌和叶片附着细菌的群落α多样性和β多样性具有显著差异.与单一植物物种体系相比,高植物物种多样性体系中植物叶片附着细菌群落α多样性较高.在高植物物种多样性体系中,黑藻叶片附着细菌群落的α多样性显著较高而β多样性显著较低,苦草叶片附着细菌群落的α多样性较低.沉水植物叶片附着细菌群落优势菌群属于变形菌门(Proteobacteria)和拟杆菌门(Bacteroidetes).高植物物种多样性体系中苦草的物种共现网络最具模块性.嗜甲基菌(g_Methylophilus)、红杆菌(f_Rhodobacter)、黄杆菌(g_Flavobacterium)是物种共现网络的关键物种.本文研究植物物种多样性对淡水湖泊细菌群落结构的影响,并强调宿主植物对附着细菌群落的重要选择作用,加深对细菌群落在水生植物叶片定殖机制的理解.;Epiphytic bacteria, adhering to the leaf surface of aquatic submerged macrophytes, develop a complex symbiotic relationship with submerged macrophytes. Epiphytic bacteria are an important component of the aquatic ecosystem, which can affect not only the growth of submerged macrophytes but also the nutrient cycling in aquatic ecosystems. Currently, the effect of submerged macrophyte diversity on the epiphytic bacteria communities is far from well understood. This study compared the effects of submerged macrophyte on bacterioplankton and epiphytic bacterial communities, meanwhile explored the community structure and diversity of epiphytic bacterial communities on different macrophytes-Vallisneria natans,Myriophyllum spicatum, Potamogeton maackianus andHydrilla verticillata. The results showed that the α diversity and structure of planktonic bacterial communities were significantly different from those of the epiphytic bacterial communities. With the increase of submerged macrophyte diversity, the α diversity of epiphytic bacterial communities increased slightly. In the systems with high submerged macrophyte diversity, significantly higher α diversity and lower β diversity were found for the epiphytic bacterial community on H. verticillata. Bacteroidetes and Proteobacteria were dominant phyla on the submerged macrophyte leaves. Co-occurrence network analysis revealed that the modularity value of V. natans epiphytic bacterial network was relatively high. Methylophilus, Rhodobacter andFlavobacterium were core species in the co-occurrence networks. This study demonstrated the effect of submerged macrophytes on bacterial community structure in freshwater lakes, emphasizing the importance of host-specific selection for epiphytic bacterial communities, and deepening our understanding of the mechanism of bacterial colonization on submerged macrophytes.

Planktonic and epiphytic bacterial communities play an important role in wetland nitrogen pollutant removal and water purification, yet their community dynamics are far from understood compared with those of the wetland soil bacterial community. Taking the planktonic bacterial community in the Yuguqiao constructed wetland and the epiphytic bacterial community on the leaf surface of the common submerged plant Vallisneria natans as the research objects, the composition, structure, and functional diversity of planktonic and epiphytic bacterial communities were analyzed using high-throughput sequencing. The results showed that the compositions of the planktonic and epiphytic bacterial communities were significantly different, with more heterotrophic and denitrifying bacteria present in the epiphytic bacterial community than in the planktonic bacterial community. The α diversity of the planktonic bacterial community was significantly different among the three sampling sites but not in the epiphytic bacterial community. In general, the OTU index and Shannon index of the epiphytic bacterial community were significantly higher than those of the planktonic bacterial community, and they had obvious spatial heterogeneity. RDA analysis showed that DO, IC, TP, NH+4, and TOC had important effects on the structural changes of both planktonic and epiphytic bacterial communities but had a greater impact on planktonic bacterial communities. Co-occurrence network analysis showed that the epiphytic bacterial community had more niche differentiation, a more stable network, and stronger resistance to external disturbance. The results of FAPROTAX functional prediction analysis showed that the nitrogen cycling, especially denitrification of the epiphytic bacterial community, was significantly greater than that of the planktonic bacterial community. The results of this study revealed the driving mechanism for maintaining the diversity of planktonic and epiphytic bacterial communities, which can provide a scientific basis for excavating and utilizing planktonic and epiphytic bacterial community resources in the construction of constructed wetlands to improve the efficiency of water purification.

This study reports on the factors involved in regulating the composition and structure of bacterial communities epiphytic on intertidal macroalgae, exploring their temporal variability and the role of copper pollution. Culture-independent, molecular approaches were chosen for this purpose and three host species were used as models: the ephemeral Ulva spp. (Chlorophyceae) and Scytosiphon lomentaria (Phaeophyceae) and the long-living Lessonia nigrescens (Phaeophyceae). The algae were collected from two coastal areas in Northern Chile, where the main contrast was the concentration of copper in the seawater column resulting from copper-mine waste disposals. We found a clear and strong effect in the structure of the bacterial communities associated with the algal species serving as host. The structure of the bacterial communities also varied through time. The effect of copper on the structure of the epiphytic bacterial communities was significant in Ulva spp., but not on L. nigrescens. The use of 16S rRNA gene library analysis to compare bacterial communities in Ulva revealed that they were composed of five phyla and six classes, with approximately 35 bacterial species, dominated by members of Bacteroidetes (Cytophaga-Flavobacteria-Bacteroides) and α-Proteobacteria, in both non-polluted and polluted sites. Less common groups, such as the Verrucomicrobiae, were exclusively found in polluted sites. This work shows that the structure of bacterial communities epiphytic on macroalgae is hierarchically determined by algal species > temporal changes > copper levels.

The contribution of host tissue location and sex to epiphytic bacterial community assembly of Sargassum thunbergii

Environmental selection and dispersal limitation are two basic processes underlying community assembly. The relative importance of those two processes differs across scales, community identities, and community types. The processes responsible for structuring microbial communities in soil of temperate subalpine forest are poorly understood. Here, we investigated the relationship between soil bacterial community structure and environmental factors, and quantified the relative role of edaphic factors, vegetation, and spatial variables in shaping the structure of six soil bacterial communities (LpMC1, LpMC2, PwMC, PmMC, PtMC, and BMC) in five forest types including Larix principis-rupprechtii, Picea wilsonii, Picea meyeri, Pinus tabulaeformis, and Betula platyphylla in Pangquangou Nature Reserve by using PCR-DGGE technology. Our results showed that the structure and biodiversity of bacterial communities were significantly different among six communities. The biodiversity of bacterial community were higher in LpMC2 and PtMC, lowest in PmMC, and highest in LpMC1. Soil environmental factors, such as pH, soil water content, total carbon, total nitrogen, soil organic matter, available phosphorous, and soil enzymes, were significantly correlated with biodiversity and structure of soil bacterial community. The beta diversity of bacterial communities were significantly correlated with geographic distance, indicating the influence of dispersal limitation on the structure of bacterial community. The order of driving force on the structure of bacterial community was edaphic factors (0.27), spatial factor (0.19) and vegetation (0.15) in six samples. Using regional soil microbes from 10 samples around reserve as source community, results from the microcosm experiments showed that the edaphic factors were the predominant driving factors (0.35) on structure of artificial dispersal bacterial community, while the high diversity of source microbial community affected the structure of microcosm soil. In summary, at local scale, environmental selection predominantly determined the structural and biodiversity of soil bacterial communities in temperate subalpine forest, while dispersal limitation played a significant role. Such a result indicated that deterministic processes and stochastic processes played important roles in shaping the structure of soil bacterial community at local scale, with the former having the leading role. The composition of dispersal soil bacteria community was source-dependent but also modulated by local environmental selection.

Alkaline lakes are a special aquatic ecosystem that act as important water and alkali resource in the arid-semiarid regions. The primary aim of the study is to explore how environmental factors affect community diversity and structure, and to find whether there are key microbes that can indicate changes in environmental factors in alkaline lakes. Therefore, four sediment samples (S1, S2, S3, and S4) were collected from Hamatai Lake which is an important alkali resource in Ordos’ desert plateau of Inner Mongolia. Samples were collected along the salinity and alkalinity gradients and bacterial community compositions were investigated by Illumina Miseq sequencing. The results revealed that the diversity and richness of bacterial community decreased with increasing alkalinity (pH) and salinity, and bacterial community structure was obviously different for the relatively light alkaline and hyposaline samples (LAHO; pH < 8.5; salinity < 20‰) and high alkaline and hypersaline samples (HAHR; pH > 8.5; salinity > 20‰). Firmicutes, Proteobacteria and Bacteriodetes were observed to be the dominant phyla. Furthermore, Acidobacteria, Actinobacteria, and low salt-tolerant alkaliphilic nitrifying taxa were mainly distributed in S1 with LAHO characteristic. Firmicutes, Clostridia, Gammaproteobacteria, salt-tolerant alkaliphilic denitrifying taxa, haloalkaliphilic sulfur cycling taxa were mainly distributed in S2, S3 and S4, and were well adapted to haloalkaline conditions. Correlation analysis revealed that the community diversity (operational taxonomic unit numbers and/or Shannon index) and richness (Chao1) were significantly positively correlated with ammonium nitrogen (r = 0.654, p < 0.05; r = 0.680, p < 0.05) and negatively correlated with pH (r = −0.924, p < 0.01; r = −0.800, p < 0.01; r = −0.933, p < 0.01) and salinity (r = −0.615, p < 0.05; r = −0.647, p < 0.05). A redundancy analysis and variation partitioning analysis revealed that pH (explanation degrees of 53.5%, pseudo-F = 11.5, p < 0.01), TOC/TN (24.8%, pseudo-F = 10.3, p < 0.05) and salinity (9.2%, pseudo-F = 9.5, p < 0.05) were the most significant factors that caused the variations in bacterial community structure. The results suggested that alkalinity, nutrient salt and salinity jointly affect bacterial diversity and community structure, in which one taxon (Acidobacteria), six taxa (Cyanobacteria, Nitrosomonadaceae, Nitrospira, Bacillus, Lactococcus and Halomonas) and five taxa (Desulfonatronobacter, Dethiobacter, Desulfurivibrio, Thioalkalivibrio and Halorhodospira) are related to carbon, nitrogen and sulfur cycles, respectively. Classes Clostridia and Gammaproteobacteria might indicate changes of saline-alkali conditions in the sediments of alkaline lakes in desert plateau.

Current Australian legislation permits the beneficial application of grease trap waste (GTW) to agricultural soil, viewing it as a beneficial source of organic matter and soil conditioner containing no/low amounts of metals or pathogenic organisms. However, little is known about the influence of GTW on soil bacterial community. A field experiment was established at Menangle in south western Sydney in Australia to quantitatively assess the impacts of different types (GTW CO and GTW CL) and amounts of GTW application on the soil bacterial community and diversity. Furthermore, a municipal solid waste (MSW) compost was simultaneously examined to compare against the other organic wastes. Knowledge about the shifts in microbial community structure and diversity following the applications of organic wastes could help to evaluate the ecological consequences on the soil and thus to develop sound regulatory guidelines for the beneficial reuse of organic wastes in agricultural lands. Soil samples were collected from recycled organics plots treated with different types and quantity of organic wastes. The field experimental treatments included control (CK, without application of any organic wastes), low amount of GTW CO (COL), GTW CL (CLL), and MSW (ML), and high amounts of GTW CO (COH), GTW CL (CLH), and MSW compost (MH). Microbial DNA was extracted from soil samples and the 16S rRNA genes were polymerase chain reaction (PCR)-amplified. The PCR products were analyzed by denaturing gradient gel electrophoresis (DGGE), cloning, and sequencing. The bacterial community structures and diversity were assessed using the DGGE profiles and clone libraries constructed from the excised DGGE bands. DGGE-based analyses showed that application of the GTW CO, regardless of the amount applied, had significant negative effects on soil bacterial genotypic diversity and community structure compared with the control, while the applications of other organic wastes including the GTW CL and MSW had no clear effects. The effects of the rate of organic waste application on soil bacterial community characteristics varied with the types of organic wastes applied. Sequence-based analyses of 126 clones indicated that Proteobacteria (53.2%) was the dominant taxa at the experimental site, followed by Actinobacteria (9.5%), Bacteroidetes (7.9%), Firmicutes (7.9%), Gemmatimonadetes (5.6%), Chloroflexi (2.4%), Acidobacteria (1.6%) and the unclassified group (11.9%). In the COH treatment, Acidobacteria, Bacteroidetes, and Gemmatimonadetes were not detected; the percentages of Firmicutes, Proteobacteria, and Actinobacteria in the COH treatment were significantly different from those in CK. There is a significant positive correlation (r = 0.71, p = 0.002) between the C/N ratio of organic wastes and the bacterial genotypic communities. Both the type and the amount of GTW applied affected soil bacterial genotypic diversity and community structure. The different effects of various types of organic wastes on soil bacterial characteristics may be predicted by the differences in specific properties of organic wastes such as C/N ratio, as evidenced by the strong and significant positive relationship between the bacterial community distance and the environmental distance of C/N ratio. This also indicates that the C/N ratio of GTW applied can be a major driver for the shift in the soil bacterial community. Our results revealed that the effects of organic wastes on soil bacterial communities varied with the types of organic wastes, and depending on the rate of application. Application of the GTW CO led to significant shifts in soil bacterial community diversity and structure. The effects of different types of organic wastes on the soil bacterial characteristics can be predicted by the differences of specific properties of organic wastes, such as the C/N ratio. Sequence-based analyses of 126 clones indicated that Proteobacteria was the dominant taxa at the experimental site. Our results have important implications for developing sound regulatory guidelines for the beneficial reuse of organic wastes, indicating that GTW CO and similar organic waste treatments may not be suitable for application in agricultural soils due to its significant negative effect on soil bacterial community.

This study examined the effect of dissolved organic matter (DOM) on ectoenzymatic activity, bacterial growth and community structure in the Hudson River. Our main approach was to mix bacterial communities and water from various locations in the Hudson River and its tributaries, and then to monitor bacterial activity and community structure determined by fluorescence in situ hybridization with oligonucleotide probes. The locations differed significantly in DOM composition and concentrations, ectoenzyme activity and bacterial community structure. We found that water source and, to a lesser extent, source of the inoculum significantly affected nearly all aspects of bacterial activity and community structure. A common inoculum grown in different waters often led to as much as a 2-fold difference in enzyme activities. When 2 different bacterial communities were inoculated in the same water, community structure and the activity of some ectoenzymes remained different after several days. Other data also pointed to a dependence of ectoenzyme activity on community structure. Activity of several ectoenzymes covaried with the relative abundances of the 4 bacterial groups we examined (alpha-, beta- and gamma-proteobacteria, and Cytophaga-like bacteria); the highest correlation was between beta-proteobacteria and phosphatase activity. In multi-variate regression analyses, community structure explained a significant amount of the variation in rates of all ectoenzymes except 2 proteases. The abundance of Cytophaga-like bacteria was the dominant variable in the regression models for the activity of 3 ectoenzymes. These data suggest that DOM can affect the relative abundance of the major heterotrophic bacterial groups, and that the relative abundance of these groups could have an impact on DOM hydrolysis.

ABSTRACTAt present, growth-promoting antibiotics are banned in the pig industry in many countries, but therapeutic antibiotics can still be used normally. However, the effect of therapeutic antibiotics on the structure and function of the intestinal bacterial community and its recovery is still unclear. We analyzed the effects of enrofloxacin on the pig manure bacterial community and functional genes during dosing and without dosing. Enrofloxacin caused significant changes in community structure. The changes in the diversity and structure of the bacterial community were the most obvious on the fifth day, and most of the differentially abundant genera (19/29) belonged to Firmicutes. The structure of the manure bacterial community in the low concentration enrofloxacin group was completely reverted after 10 days of drug discontinuation. In addition, enrofloxacin had a significant impact on the abundance of bacterial functional genes. Most of the differentially abundant functional genes of the manure bacterial community were significantly enriched, especially genes related to metabolic pathways, for adaptation to the antibiotic environment. Moreover, exposure to enrofloxacin increased the abundance of functional genes related to nitrogen metabolism in the manure bacterial community, and the total nitrogen content of pig manure was significantly reduced. The functional genetic differences caused by enrofloxacin exposure were completely reverted 10 days after drug discontinuation. The results of the present study suggest that enrofloxacin induces changes in the structure and function of manure bacterial communities, which may be rapidly recovered after drug discontinuation.IMPORTANCE A stable intestinal bacterial community balance is beneficial for animal health. Enrofloxacin is widely used in animal husbandry as a therapeutic drug, but it can cause intestinal environmental imbalance. Enrofloxacin is widely present in groundwater, pork, etc., which leads to a greater risk of human exposure. The effect of enrofloxacin on the structure and function of the intestinal bacterial community and its recovery is still unclear. In this study, we found that enrofloxacin, as a therapeutic drug, can enhance nitrogen metabolism in the manure bacterial community. Moreover, the structure and function of the manure bacterial community in the low concentration enrofloxacin group may be completely reverted 10 days after drug discontinuation. This study provides a reference for the effect of enrofloxacin exposure on the intestinal bacterial community.

The purpose of this study was to ascertain the epiphytic bacterial community structure of macroalgae Gongolaria barbata (Stackhouse) Kuntze samples taken from seawater using Single Strand Conformation Polymorphism (SSCP) analysis. It also aims to quickly obtain information regarding the composition of communities and the quality of the seawater. G. barbata samples were subjected to total DNA extraction, SSCP analysis was conducted with a focus on the V4-V5 region of 16S rRNA, and the bacterial community structure was determined through sequence analysis of a few chosen bands. Upon analyzing the SSCP gel picture and dendrogram, it was seen that the bacterial community structure on the macroalgae varied based on the location as well as within the same species. It was noted that the Gammaproteobacteria class accounted for 84.375 percent of the bands that were acquired from the SSCP analysis. The fact that the sequencing data generated from the bands collected at various points largely resembled Vibrio and Klebsiella genera was notable. This situation highlights the strong link between harmful or opportunistic infectious organisms and macroalgae species, several of which have been suggested for ingestion as food. Furthermore, even if research in the literature suggests that the macroalgae and the microbial load of the nearby water sample do not significantly correlate, we can conclude that this data suggests the possibility of risk.

Composition of soil viral and bacterial communities after long-term tillage, fertilization, and cover cropping management

Core Ideas The selected enzymatic activities were not significantly affected by the GK 12. The bacterial population size was not significantly affected by the GK 12. The bacterial community structure was not significantly affected by the GK 12. Transgenic Bt‐cotton (Gossypium hirsutum L.) GK 12 is commonly used for control of lepidopteran pests in China, but concerns exist regarding possible unintended effects on soil microbial communities. Bacterial population sizes and community structures in the rhizosphere soil under intensive cultivation of GK 12, its near‐isogenic parent Simian 3 and a conventional cotton DP 5415 were analyzed during 2009 to 2011 by quantitative polymerase chain reaction (qPCR) and denaturing gradient gel electrophoresis (DGGE). Dehydrogenase, urease, and phosphatase activities were also measured. It was found that these microbial‐related parameters were significantly influenced by variations due to the year and plant growth stage. There were occasional differences in bacterial population size and community structures at some growth stages, but they were not manifested throughout the growing cycle and were not considered meaningful. Generally no significant differences were found in selected enzymatic activities, and bacterial population sizes and community structures in the rhizosphere soil of GK 12 and Simian 3. Three different species or bands were unique to GK 12 and Simian 3, but they were unamplifiable. The resolvable band profile or annotatable species composition was not different between GK 12 and Simian 3. Therefore, the data of this study did not show any significant and permanent impacts of Bt‐insertion in GK 12 on selected enzymatic activities, bacterial population size, and community structures in the rhizosphere soil during 3‐yr tests in northern China.

Salinity is a key determinant governing microalgal growth, biochemical composition, and the structure of associated epiphytic bacterial communities. To investigate the effects of salinity on the structure and function of the epiphytic bacterial community in Desmodesmus intermedius, this study utilized 16S rRNA gene high-throughput sequencing to analyze the communities across the control (S0) and experimental groups (S5, S10, S15). The results demonstrated that salinity is a key environmental driver governing the structural and functional succession of the bacterial community. Alpha diversity analysis revealed that the control group exhibited the highest bacterial diversity and greater evenness. In contrast, the experimental groups showed a significant increase in the relative abundance of Thauera and a concurrent decrease in Roseococcus with increasing salinity. Beta diversity analysis revealed clear segregation of the epiphytic bacterial communities across the salinity groups. FAPROTAX functional prediction revealed that increasing salinity led to a reduction in chemoheterotrophy, photoheterotrophy, and aerobic chemoheterotrophy, while enhancing nitrogen respiration, nitrate reduction, and other denitrification processes. This shift indicates a substantial reconfiguration of carbon and nitrogen metabolic pathways. BugBase phenotype analysis further revealed that the experimental groups exhibited a higher proportion of Gram-positive bacteria and enhanced biofilm-forming capacity. Canonical correspondence analysis identified salinity as the predominant factor shaping bacterial community structure. This study comprehensively investigates the response mechanisms of the D. intermedius epiphytic bacterial community to salt stress, laying a foundation for understanding microbial functions within the phycosphere.

As vertebrate carrion decomposes, there is a release of nutrient-rich fluids into the underlying soil, which can impact associated biological community structure and function. How these changes alter soil biogeochemical cycles is relatively unknown and may prove useful in the identification of carrion decomposition islands that have long lasting, focal ecological effects. This study investigated the spatial (0, 1, and 5 m) and temporal (3–732 days) dynamics of human cadaver decomposition on soil bacterial and arthropod community structure and microbial function. We observed strong evidence of a predictable response to cadaver decomposition that varies over space for soil bacterial and arthropod community structure, carbon (C) mineralization and microbial substrate utilization patterns. In the presence of a cadaver (i.e., 0 m samples), the relative abundance of Bacteroidetes and Firmicutes was greater, while the relative abundance of Acidobacteria, Chloroflexi, Gemmatimonadetes, and Verrucomicrobia was lower when compared to samples at 1 and 5 m. Micro-arthropods were more abundant (15 to 17-fold) in soils collected at 0 m compared to either 1 or 5 m, but overall, micro-arthropod community composition was unrelated to either bacterial community composition or function. Bacterial community structure and microbial function also exhibited temporal relationships, whereas arthropod community structure did not. Cumulative precipitation was more effective in predicting temporal variations in bacterial abundance and microbial activity than accumulated degree days. In the presence of the cadaver (i.e., 0 m samples), the relative abundance of Actinobacteria increased significantly with cumulative precipitation. Furthermore, soil bacterial communities and C mineralization were sensitive to the introduction of human cadavers as they diverged from baseline levels and did not recover completely in approximately 2 years. These data are valuable for understanding ecosystem function surrounding carrion decomposition islands and can be applicable to environmental bio-monitoring and forensic sciences.

Heavy metal pollution poses a serious hazard to the soil bacterial community. In this study, the 16 s rRNA high-throughput sequencing technology was used to analyze bacterial diversity and structure of dry field soil at different levels of heavy metal pollution. Further, the relationships between soil parameters and bacterial community were analyzed. Based on the study findings, we classified the levels of heavy metal pollution in soil samples from the study area could be divided into four grades: high risk (HR), considerable risk (CR), moderate risk (MR) and low risk (LR). In this study, heavy metal concentrations and pH showed significant effect on bacterial community structure. The distribution of bacterial community richness and diversity was MR > LR > CR > HR. Bacterial communities such as Acidobacteria, Chloroflexi and Gemmatimonadetes were highly resistant to the lower pH (pH < 6.5) and the high levels of heavy metal pollution compared with other bacterial community, which were abundant in HR samples. However, Proteobacteria, Actinobacteria, Bacteroidetes and Latescibacteria were more abundant in alkaline soils (pH > 7.5). Further, available Cd, Pb and Zn concentrations were lower in alkaline soils than acidic soils, which reduced the impact of heavy metals on bacterial community diversity and structure.