Composition of epiphytic bacterial communities differs on petals and leaves

The epiphytic bacterial communities colonising roots and leaves have been described for many plant species. In contrast, microbiologists have rarely considered flowers of naturally growing plants. We identified bacteria isolated from the surface of petals and leaves of two plant species, Saponaria officinalis (Caryophyllaceae) and Lotus corniculatus (Fabaceae). The bacterial diversity was much lower on petals than on leaves of the same plants. Moreover, the bacterial communities differed strongly in composition: while Pseudomonadaceae and Microbacteriaceae were the most abundant families on leaves, Enterobacteriaceae dominated the floral communities. We hypothesise that antibacterial floral volatiles trigger the low diversity on petals, which is supported by agar diffusion assays using substances emitted by flowers and leaves of S. officinalis. These results suggest that bacteria should be included in the interpretation of floral traits, and possible effects of bacteria on pollination are proposed and discussed.     

海水鱼类共附生细菌群落研究进展

与海水鱼类处于共生、共栖、寄生或附生关系的细菌群落,称之为海水鱼类共附生细菌群落。这类细菌群落生活在海水鱼体表(皮肤、鳃)以及体内(消化道和血液、肌肉、肝脏、肾脏等内部组织器官),它们彼此之间以及与宿主之间存在着极其密切的关系,并且对于宿主的健康生长具有重要作用。然而,由于目前对养殖系统中的微生物群落中的致病微生物缺乏有效控制措施,处于迅速发展中的养殖产业经受着相当严重的疾病问题。因而,生态健康养殖被提到议事日程上来,并且日益受到重视,其中微生物生态调控是极其重要的一个环节。由于目前相关的基础微生物生态学资料比较缺乏,尤其是在国内作为微生物生态的基本组成部分,与微生物病害发生有着直接关系的大多数海水养殖鱼类的共附生细菌群落研究资料相当缺乏。因此,很有必要开展海水养殖鱼类共附生细菌群落相关研究。在此背景下,从研究的目的和意义以及国内外研究现状包括宿主海水鱼类种类、共附生细菌群落类别、共附生细菌群落的影响因素、共附生细菌群落对宿主的作用等方面综述了海水鱼类共附生细菌群落的研究进展,并对此类研究趋势进行了展望,为开展相关研究提供一定的参考。     

Inter- and intraspecific phytochemical variation correlate with epiphytic flower and leaf bacterial communities

Microbes associated with flowers and leaves affect plant health and fitness and modify the chemical phenotypes of plants with consequences for interactions of plants with their environment. However, the drivers of bacterial communities colonizing above-ground parts of grassland plants in the field remain largely unknown. We therefore examined the relationships between phytochemistry and the epiphytic bacterial community composition of flowers and leaves of Ranunculus acris and Trifolium pratense. On 252 plant individuals, we characterized primary and specialized metabolites, that is, surface sugars, volatile organic compounds (VOCs), and metabolic fingerprints, as well as epiphytic flower and leaf bacterial communities. The genomic potential of bacterial colonizers concerning metabolic capacities was assessed using bacterial reference genomes. Phytochemical composition displayed pronounced variation within and between plant species and organs, which explained part of the variation in bacterial community composition. Correlation network analysis suggests strain-specific correlations with metabolites. Analysis of bacterial reference genomes revealed taxon-specific metabolic capabilities that corresponded with genes involved in glycolysis and adaptation to osmotic stress. Our results show relationships between phytochemistry and the flower and leaf bacterial microbiomes suggesting that plants provide chemical niches for distinct bacterial communities. In turn, bacteria may induce alterations in the plants' chemical phenotype. Thus, our study may stimulate further research on the mechanisms of trait-based community assembly in epiphytic bacteria.     

Climax epiphytic communities in Mediterranean Spain

The Antitrichetalia curtipendulae epiphytic climax communities of Šmarda & Hadàč from the Spanish Mediterranean area have been classified by numerical and traditional floristic methods. Ninety-eight phytosociological relevés have been recorded from a number of Iberian forests. Our results indicate two clusters that can be easily related to two different alliances: Lobarion pulmonariae (Nephrometum resupinati) and Pterogonio gracile-Antitrichion californicae (Antitrichielum californicae). A phytogeographical and syntaxonomical discussion is followed by a suggested Red List of threatened lichens and bryophytes occurring in these communities in the Spanish Mediterranean area with the aim of advancing conservation of endangered and vulnerable species.     

Structure of bacterial communities in diverse freshwater habitats

The structures and dynamics of bacterial communities from raw source water, groundwater, and drinking water before and after filtration were studied in four seasons of a year, with culture-independent methods. Genomic DNA from water samples was analyzed by the polymerase chain reaction?- denaturing gradient gel electrophoresis system and by cloning of the 16S rRNA gene. Water samples exhibited complex denaturing gradient gel electrophoresis genetic profiles composed of many bands, corresponding to a great variety of bacterial taxa. The bacterial communities of different seasons from the four sampling sites clustered into two major groups: (i) water before and after filtration, and (ii) source water and groundwater. Phylogenetic analyses of the clones from the autumn sampling revealed 13 phyla, 19 classes, and 155 operational taxonomic units. Of the clones, 66% showed less than 97% similarities to known bacterial species. Representatives of the phyla Proteobacteria, Bacteroidetes, and Actinobacteria were found at all four sampling sites. Species belonging to the phylum Firmicutes were an important component of the microbial community in filtered water. Representatives of Enterobacteriaceae were not detected, indicating the absence of fecal pollution in the drinking water. Differences were found in the bacterial populations that were sampled from the same sites in different seasons. Each water habitat had a unique bacterial profile. Drinking water harbors diverse and dynamic microbial communities, part of which may be active and resilient to chlorine disinfection. This study provides, for the first time, basic data for uncultivable drinking water bacteria in Israel.     

Seasonal dynamics of the structure of epiphytic yeast communities

The seasonal dynamics of the species structure of epiphytic yeasts on the leaves and in the flowers of 25 plant species was studied throughout the period of their vegetation. It was shown that, on average for the vegetation period, the composition of epiphytic yeast communities was nonspecific. The same species of epiphytic yeasts dominated on different plant species, irrespective of their taxonomic identity and ecological peculiarities. However, different species of yeasts exhibited different types of seasonal dynamics of relative abundance. Therefore, a combination of the dynamics of yeast species and the ontogenetic cycles of plants creates a pattern of the dynamics of the epiphytic yeast population, which is unique for each plant species. The species diversity of yeasts on the leaves of a plant is determined by the duration of its ontogenetic cycle: the longer the vegetation of a plant, the higher the diversity of the epiphytic yeasts population. The greatest diversity of epiphytic yeasts was revealed on the leaves of perennial hygrophytes and mesophytes; the minimal diversity, on ephemeroids and annuals with a short ontogenetic cycle.     

Accumulation of detached kelp biomass in a subtidal temperate coastal ecosystem induces succession of epiphytic and sediment bacterial communities

Kelps are dominant primary producers in temperate coastal ecosystems. Large amounts of kelp biomass can be exported to the seafloor during the algal growth cycle or following storms, creating new ecological niches for the associated microbiota. Here, we investigated the bacterial community associated with the kelp Laminaria hyperborea during its accumulation and degradation on the seafloor. Kelp tissue, seawater and sediment were sampled during a 6-month in situ experiment simulating kelp detritus accumulation. Evaluation of the epiphytic bacterial community abundance, structure, taxonomic composition and predicted functional profiles evidenced a biphasic succession. Initially, dominant genera (Hellea, Litorimonas, Granulosicoccus) showed a rapid and drastic decrease in sequence abundance, probably outcompeted by algal polysaccharide-degraders such as Bacteroidia members which responded within 4 weeks. Acidimicrobiia, especially members of the Sva0996 marine group, colonized the degrading kelp biomass after 11 weeks. These secondary colonizers could act as opportunistic scavenger bacteria assimilating substrates exposed by early degraders. In parallel, kelp accumulation modified bacterial communities in the underlying sediment, notably favouring anaerobic taxa potentially involved in the sulfur and nitrogen cycles. Overall, this study provides insights into the bacterial degradation of algal biomass in situ, an important link in coastal trophic chains.     

Structure and diversity of bacterial communities in the fermentation of da-jiang

Da-jiang is the traditional soybean fermented food which is popular in the world for a long time. In order to improve the quality and nutritional value of da-jiang, structure and diversity of bacterial communities in the fermentation of da-jiang were analyzed. Illumina MiSeq platforms coupled with bioinformatics approach were used in this study. In the first 28 days, the trends of bacterial abundance were similar in different regions which are increasing firstly, decreasing secondly, and rising again. The quantity of bacteria in post-fermentation is lower than pre-fermentation. In the fermentation of da-jiang, Firmicutes and Proteobacteria are the dominant phyla. The dominant genera in da-jiang from different regions are different: Tetragenococcus (58.1–73.0%) is the dominant genus in da-jiang from Xinmin; Leuconostoc (9.2–25.7%) is the dominant genus in da-jiang from Tieling; Acinetobacter (8.7–25.1%) and Leuconostoc (12.4–22.0%) are the dominant genera in da-jiang from Shenyang. Additionally, Weissella, Lactobacillus, Staphylococcus, Erwinia, and Pseudomonas also were found in da-jiang. It is identified that Leuconostoc steadily existed in all da-jiang samples. These results demonstrate the diversity of microbes in traditional fermented da-jiang, which will probably provide a data basis for choosing starter culture for da-jiang industrial fermentation.     

Gastropod grazing of epiphytic lichen-dominated communities depends on tree species

Tree species differ in longevity, canopy structure, and bark texture, chemistry and water storage. Tree species-specific traits play a role in shaping epiphytic vegetation and likely influence the community assembly of organisms feeding on epiphytes. Lichenivorous gastropods, species with calcium-rich shells in particular, need calcium and likely occur more abundantly in and around tree species with high available calcium. We quantified gastropod grazing on the epiphytic lichens Lobaria pulmonaria and Lobaria scrobiculata transplanted to blocks of adjacent trunks of Acer platanoides, Quercus robur and Tilia cordata. We tested the hypothesis that tree species known to have more available Ca, exhibit more grazing damage on transplanted lichens than trees with lower Ca-availability. The grazing pressure was 1.6–1.8 times higher for lichen transplants on Acer and Tilia known to produce litter with easily soluble Ca than on Quercus, which binds Ca as oxalate. Trees with a high grazing pressure on transplants had greater natural abundance of Lobaria virens than of L. pulmonaria. Gastropods preferred L. scrobiculata to L. pulmonaria, evidenced by more observed grazing marks and greater measured biomass loss. We attribute this difference to the lower concentration of carbon-based secondary compounds in L. scrobiculata. However, the strength of the preference varied between the three tree species receiving lichen transplants and was strongest on A. platanoides, while gastropods on T. cordata grazed equal amounts of each transplanted lichen. In conclusion, tree species influenced grazing patterns of gastropods on epiphytic lichens. In addition to bark pH and other factors, we have shown that tree species-specific differences in grazing pressure play a role in shaping the epiphytic macrolichen community.     

Associations between corticolous microarthropod communities and epiphytic cover on bark

The discontinuous bark cover formed by epiphytic lichens and algae provides a mosaic of microhabitats for the fauna. Multivariate analyses applied to 1800 samples collected in Belgian Lorraine (southern Belgium) during each of the four seasons has made it possible to distinguish five major classes of arthropod microcommunities. Two of them are confined to special habitats or places at certain seasons, viz.

• –

  a Pseudochermes fraxini (Homoptera) community found on Fraxinus during the summer, and "trophically" different from others;
• –

  a Vertagopus arborea (Collembola) community observed in foliose lichens in St. Mard mainly in winter.

The three other classes are directly related to the epiphytic cover, viz.

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  a Dometorina plantivaga (Oribatida) community found in crustose epiphytes;
• –

  an Eueremaeus oblongus/Trichoribates trimaculatus (Oribatida) community sheltered by foliose lichens;
• –

  an Entomobrya nivalis (Collembola)/Cerobasis guestfalicus (Psocoptera) community observed in fruticose lichens.

The ecological meaning of those microcommunities (mosaic and stratification patterns, seasonal variation, succession) is discussed. The results support the hypothesis that corticolous microcoenoses are associated with the epiphyte type and that their composition is greatly affected by the vegetation stratification pattern on bark.     

An analysis of epiphytic lichen communities in Tasmanian cool temperate rainforest

A three-dimensional compositional pattern in the epiphytic lichen vegetation in Tasmanian cool temperate rainforest is demonstrated using the robust ordination technique, hybrid multidimensional scaling (HMDS). The first two dimensions are correlated with the age of the host tree (and the concomitant change in bark texture) and wetness of the substrate. No measured environmental variable is related to the third dimension, which is tentatively attributed to a gradient in the constancy of the microclimate. Patterns of richness of lichen growth forms and the cover of bryophytes are correlated with the three putative environmental gradients. Possible successional trends between 12 community groups derived by numerical classification are described with respect to changes in substrate age, wetness and microclimatic constancy. Temporal variation of these factors due to tree growth, together with the slow establishment and long persistence of some lichen species, make succession in epiphytic communities very complex. This study demonstrates the value of HMDS in identifying compositional patterns and generating hypotheses about the causal ecological factors. The existence of the postulated microclimatic constancy gradient was not appreciated before the analysis and its discovery illustrates the risk of relying on constrained ordination methods, such as canonical correspondence analysis.Abbreviations HMDS Hybrid multidimensional scaling - NMDS Non-metric multidimensional scaling     

茶园根际土壤细菌群落结构及多样性

【背景】茶园根际土壤的细菌群落结构与茶园生境土壤营养循环密切相关,其组成及多样性可以作为健康茶园的一个生物指标。【方法】采用PCR．变性梯度凝胶电泳（PCR—DGGE）分子指纹图谱技术,检测安溪铁观音种植区不同海拔茶园根际土壤样本的细菌群落结构,利用Shannon．Wiener多样性指数分析其多样性,采用非加权组平均法进行聚类分析得到其分布特征,利用蒙特卡罗检验和冗余分析分别揭示影响细菌群落分布的环境因子及细菌群落分布和环境变量之间的关系。【结果】茶园根际土壤细菌的DGGE结果显示,检测到的14种主要细菌中有11种细菌是不可培养的,3种细菌是可培养的,分别属于根瘤菌属、中华根瘤菌属和苍白杆菌属。聚类分析得到,同一海拔梯度茶园根际土壤细菌群落结构相似。Shan-non—Wiener多样性指数分析表明,400m海拔处茶园根际土壤细菌群落多样性最高。蒙特卡罗检验分析得到环境因子协同作用对茶园根际土壤细菌群落结构贡献率为59．6％。冗余分析显示,茶园根际土壤细菌群落结构与海拔密切相关。【结论与意义】茶园根际土壤细菌群落结构分布与海拔梯度密切相关,考虑不同海拔高度土壤细菌群落对茶园营养循环的影响,在铁观音的健康栽培和管理过程中具有重要意义。     

Structure and function of bacterial communities emerging from different sources under identical conditions

The aim of this study was to compare two major hypotheses concerning the formation of bacterial community composition (BCC) at the local scale, i.e., whether BCC is determined by the prevailing local environmental conditions or by "metacommunity processes." A batch culture experiment where bacteria from eight distinctly different aquatic habitats were regrown under identical conditions was performed to test to what extent similar communities develop under similar selective pressure. Differently composed communities emerged from different inoculum communities, as determined by terminal restriction fragment length polymorphism analysis of the 16S rRNA gene. There was no indication that similarity increased between communities upon growth under identical conditions compared to that for growth at the ambient sampling sites. This suggests that the history and distribution of taxa within the source communities were stronger regulating factors of BCC than the environmental conditions. Moreover, differently composed communities were different with regard to specific functions, such as enzyme activities, but maintained similar broad-scale functions, such as biomass production and respiration.     

Structure of bacterial communities along a hydrocarbon contamination gradient in a coastal sediment

The bacterial diversity of a chronically oil-polluted retention basin sediment located in the Berre lagoon (Etang-de-Berre, France) was investigated. This study combines chemical and molecular approaches in order to define how the in situ petroleum hydrocarbon contamination level affects the bacterial community structure of a subsurface sediment. Hydrocarbon content analysis clearly revealed a gradient of hydrocarbon contamination in both the water and the sediment following the basin periphery from the pollution input to the lagoon water. The nC17 and pristane concentrations suggested alkane biodegradation in the sediments. These results, combined with those of terminal-restriction fragment length polymorphism analysis of the 16S rRNA genes, indicated that bacterial community structure was obviously associated with the gradient of oil contamination. The analysis of bacterial community composition revealed dominance of bacteria related to the Proteobacteria phylum (Gamma-, Delta-, Alpha-, Epsilon- and Betaproteobacteria), Bacteroidetes and Verrucomicrobium groups and Spirochaetes, Actinobacteria and Cyanobacteria phyla. The adaptation of the bacterial community to oil contamination was not characterized by dominance of known oil-degrading bacteria, because a predominance of populations associated to the sulphur cycle was observed. The input station presented particular bacterial community composition associated with a low oil concentration in the sediment, indicating the adaptation of this community to the oil contamination.     

Neutral assembly of bacterial communities

Two recent, independent advances in ecology have generated interest and controversy: the development of neutral community models (NCMs) and the extension of biogeographical relationships into the microbial world. Here these two advances are linked by predicting an observed microbial taxa-volume relationship using an NCM and provide the strongest evidence so far for neutral community assembly in any group of organisms, macro or micro. Previously, NCMs have only ever been fitted using species-abundance distributions of macroorganisms at a single site or at one scale and parameter values have been calibrated on a case-by-case basis. Because NCMs predict a malleable two-parameter taxa-abundance distribution, this is a weak test of neutral community assembly and, hence, of the predictive power of NCMs. Here the two parameters of an NCM are calibrated using the taxa-abundance distribution observed in a small waterborne bacterial community housed in a bark-lined tree-hole in a beech tree. Using these parameters, unchanged, the taxa-abundance distributions and taxa-volume relationship observed in 26 other beech tree communities whose sizes span three orders of magnitude could be predicted. In doing so, a simple quantitative ecological mechanism to explain observations in microbial ecology is simultaneously offered and the predictive power of NCMs is demonstrated.     

A simple apparatus for sampling epiphytic communities associated with emergent macrophytes

The apparatus allows the sampling of both algal and animal components of the epiphyton. It consists of a perspex tube, 100 cm long with an internal diameter of 4 cm, and of an epiphytic sieve. The latter is made of two 2.5 cm cross-sections of perspex tubing with a piece of circular mesh glued between them. While sampling, a randomly chosen shoot is isolated from the ambient water by means of the tube, cut at the bottom sediment and removed together with epiphyton. The water, taken together with the shoot is then removed using the epiphytic sieve, joined with the tube under the water surface. The detached organisms, associated with the stem and those scraped from the stem with a stiff brush afterwards, concentrate on the mesh.     

Edge effects on epiphytic communities in a Mediterranean Quercus pyrenaica forest

Question: What are the edge effect responses of epiphytic lichen communities in Mediterranean Quercus pyrenaica forest? Location: Central Spain. Methods: We established ten transects perpendicular to a road dissecting a well conserved remnant of Q. pyrenaica forest into two sections. Transects extended from the forest/road edge to 100 m into the forest. Data were collected from seven plots in each transect at different distances from the edge. Variables were grouped into stand scale variables (distance to edge, number of trees per plot, mean diameter per plot, irradiance) and tree scale variables (diameter and height of sampled trees, aspect of the sampled square and relative height of the square). We used General Mixed Linear Models and constrained ordination techniques to test the hypothesis that the spatio‐temporal heterogeneity of light and water controls the occurrence of lichens and bryophytes along the edge‐interior gradient in the Q. pyrenaica forest. Results: Microclimatic parameters vary in a non‐linear way; edge and interior stands showed the most divergent and extreme values. Although the micro‐environment within Mediterranean forests is heterogeneous, interior conditions are apparently suitable for the performance of some specific forest epiphytes. Consequently, species richness does not show significant differences along the gradient. Total epiphytic cover increases towards the forest interior, but distance to the edge together with other predictors at the tree scale (aspect and height of the square) are the most relevant predictors for the composition and structure of these communities. Conclusions: Composition and structure of epiphytic communities in a Mediterranean semi‐deciduous forest are affected by the edge between the forest and the road constructed. Since some extremely rare lichens only occur at interior stands, the conservation of these threatened elements requires urgent conservation measures because well preserved and unmanaged forests in the Mediterranean region are very rare.