Seasonal and vertical distribution of planktonic bacteria and heterotrophic nanoflagellates in the middle Adriatic Sea

Temporal and spatial patterns of bacteria and heterotrophic nanoflagellates (HNF) were studied monthly from January 1997 to December 1998 in the middle Adriatic Sea. Bacterial and HNF relationships with phytoplankton biomass and temperature were analyzed to examine how the relative importance of bottom-up and top-down factors may shift over seasons and locations. For the coastal area, an inconsistent relationship between bacterial abundance and chlorophyll a and a stronger relationship between bacterial abundance and bacterial production suggest that other substrates than those of phytoplankton origin are important for bacteria. The analysis of simultaneous effects of temperature and bacterial production on bacterial abundance showed that the effect of temperature obscured the effects of bacterial production, suggesting that bacterial growth itself is highly temperature-dependent. The relationship between HNF abundance and bacterial abundance was slightly improved by the inclusion of in situ temperature, bacterial production or both parameters, as additional independent variables. About 60% of the variability in HNF abundance can be explained by bacterial abundance, bacterial production and temperature. In the open sea, tight coupling of bacterial abundance with chlorophyll a concentrations implied that phytoplankton-derived substrates have a dominant role in controlling bacterial abundance. During the colder months, bacterial abundance was high enough to support higher HNF abundance than observed, suggesting that predation exerted a minor depressing influence on bacterial abundance during that period. During the spring-summer period, HNF controlled bacterial standing stocks by direct cropping of bacterial production.Communicated by: H.-D. Franke     

Species-sorting may explain an apparent minimal effect of immigration on freshwater bacterial community dynamics

Long distance atmospheric transport of bacterial cells is often implied as a driver of the apparent cosmopolitan distribution of bacterial taxa. Surprisingly, efforts to measure immigration in bacterial communities are rare. An 8-week time series of within-lake bacterial community composition and atmospheric deposition rates and composition were used to estimate the influence of immigration on bacterial community dynamics in two north temperate lakes. Characterization of bacterial community dynamics using automated ribosomal intergenic spacer analysis suggested moderate overlap in composition between the lakes and atmospherically deposited cells. However, taxa that appeared to be delivered by atmospheric deposition had a relatively minor influence on lake bacterial community dynamics. The weak influence of immigrating bacterial taxa suggests that a species-sorting concept best describes aquatic bacterial metacommunity dynamics.     

Bacteria, phages and septicemia

The use of phages is an attractive option to battle antibiotic resistant bacteria in certain bacterial infections, but the role of phage ecology in bacterial infections is obscure. Here we surveyed the phage ecology in septicemia, the most severe type of bacterial infection. We observed that the majority of the bacterial isolates from septicemia patients spontaneously secreted phages active against other isolates of the same bacterial strain, but not to the strain causing the disease. Such phages were also detected in the initial blood cultures, indicating that phages are circulating in the blood at the onset of sepsis. The fact that most of the septicemic bacterial isolates carry functional prophages suggests an active role of phages in bacterial infections. Apparently, prophages present in sepsis-causing bacterial clones play a role in clonal selection during bacterial invasion.     

Minerals in soil select distinct bacterial communities in their microhabitats

We tested the hypothesis that different minerals in soil select distinct bacterial communities in their microhabitats. Mica (M), basalt (B) and rock phosphate (RP) were incubated separately in soil planted with Trifolium subterraneum, Lolium rigidum or left unplanted. After 70 days, the mineral and soil fractions were separated by sieving. Automated ribosomal intergenic spacer analysis was used to determine whether the bacterial community structure was affected by the mineral, fraction and plant treatments. Principal coordinate plots showed clustering of bacterial communities from different fraction and mineral treatments, but not from different plant treatments. Permutational multivariate anova ( permanova ) showed that the microhabitats of M, B and RP selected bacterial communities different from each other in unplanted and L. rigidum , and in T. subterraneum , bacterial communities from M and B differed ( P <0.046). permanova also showed that each mineral fraction selected bacterial communities different from the surrounding soil fraction ( P <0.05). This study shows that the structure of bacterial communities in soil is influenced by the mineral substrates in their microhabitat and that minerals in soil play a greater role in bacterial ecology than simply providing an inert matrix for bacterial growth. This study suggests that mineral heterogeneity in soil contributes to the spatial variation in bacterial communities.     

Nonradioactive method to study genetic profiles of natural bacterial communities by PCR-single-strand-conformation polymorphism.

We describe a new method for studying the structure and diversity of bacterial communities in the natural ecosystem. Our approach is based on single-strand-conformation polymorphism (SSCP) analysis of PCR products of 16S rRNA genes from complex bacterial populations. A pair of eubacterial universal primers for amplification of the variable V3 region were designed from the 16S rRNA sequences of 1,262 bacterial strains. The PCR conditions were optimized by using genomic DNAs from five gram-positive and seven gram-negative strains. The SSCP analysis of the PCR products demonstrated that a bacterial strain generated its characteristic band pattern and that other strains generated other band patterns, so that the relative diversity in bacterial communities could be measured. In addition, this method was sensitive enough to detect a bacterial population that made up less than 1.5% of a bacterial community. The distinctive differences between bacterial populations were observed in an oligotrophic lake and a eutrophic pond in a field study. The method presented here, using combined PCR amplification and SSCP pattern analyses of 16S rRNA genes, provides a useful tool to study bacterial community structures in various ecosystems.     

Distinct successional patterns and processes of free-living and particle-attached bacterial communities throughout a phytoplankton bloom

1. Understanding the successional patterns of microbial communities during a phytoplankton bloom is crucial for predicting the compositional and functional stability of lake ecosystems in response to the disturbance of a bloom. Previous studies on bacterial communities associated with blooms have rarely studied the dynamics of these communities. The successional patterns of bacterial communities within different micro-habitats (i.e. water column versus particles) and mechanisms that shape these communities that differ in composition and structure remain unclear.
2. We selected a eutrophic urban lake to investigate the succession of bacterial communities during a bloom. We divided the bacterial communities into free-living (FL) and particle-attached (PA) groups based on their different lifestyles. The amplicon-based 16S rRNA gene high-throughput sequencing technology was used to obtain bacterial community composition and phylogenetic structure.
3. Our study showed distinct successional patterns between FL and PA bacterial communities, and the two bacterial lifestyles showed different responses and resilience to the bloom, in terms of diversity and relative abundance of bacterial taxa. Alpha-diversity of the PA bacterial community decreased during the bloom, whereas that of the FL bacterial community increased. More taxa in the FL bacterial community showed resilience after the disturbance than in the PA bacterial community.
4. The influence of phytoplankton blooms on the assembly of the bacterial community can be viewed as niche selection that led to the decrease in the relative importance of stochastic processes in shaping both FL and PA bacterial communities. This study shows the ecological significance of the bacterial community response to bloom events in lakes. It also shows that assembly processes differ for bacterial communities that have different lifestyles in lake ecosystems disturbed by phytoplankton blooms.

     

Nutritional influences on the gut microbiota and the consequences for gastrointestinal health

The human colonic microbiota degrades dietary substrates that are indigestible in the upper GIT (gastrointestinal tract), releasing bacterial metabolites, some of which are important for gut health. Advances in molecular biology techniques have facilitated detailed analyses of the composition of the bacterial community resident in the lower GIT. Such analyses have indicated that more than 500 different bacterial species colonize an individual, and that, although there is much functional consistency in the resident bacterial groups, there is considerable inter-individual variation at the species/strain level. The bacterial community develops during early childhood until it reaches an adult-like composition. Whereas colonization and host factors influence the species composition, dietary factors also have an important impact, with specific bacterial groups changing in response to specific dietary interventions. Since bacterial species have different metabolic activities, specific diets have various consequences for health, dependent on the effect exerted on the bacterial population.     

Autophagy and bacterial clearance: a not so clear picture

Autophagy, an intracellular degradation process highly conserved from yeast to humans, is viewed as an important defence mechanism to clear intracellular bacteria. However, recent work has shown that autophagy may have different roles during different bacterial infections that restrict bacterial replication (antibacterial autophagy), act in cell autonomous signalling (non‐bacterial autophagy) or support bacterial replication (pro‐bacterial autophagy). This review will focus on newfound interactions of autophagy and pathogenic bacteria, highlighting that, in addition to delivering bacteria to the lysosome, autophagy responding to bacterial invasion may have a much broader role in mediating disease outcome.     

3种革兰氏阴性细菌及其L型内毒素含量的测定

本文采用鲎试剂对大肠杆菌（ＡＴＣＣ２５９２２）、伤寒杆菌、绿脓杆菌（ＡＴＣＣ７８５３）及它们的Ｌ型内毒素的含量进行测定。结果显示细菌型与细菌Ｌ型均具有内毒素,但细菌Ｌ型内毒素含量较细菌型低（约为１／３￣１／２）。因此,认为细菌Ｌ型仍有一定的致病性。     

The effects of nematodes on bacterial activity and abundance in a freshwater sediment

The effects of natural nematode communities on bacterial activity and abundance were investigated in a microcosm study. Nematodes were added at different densities to a freshwater sediment and bacterial parameters were measured after 1, 5, 9, and 17 days. Significant effects of nematode density on bacterial activity were noted on day 5. No long-term changes in bacterial activity were recorded. Bacterial abundance displayed an overall decrease in both treatments and controls. In a second experiment, the effect of nematode feeding-type on bacterial activity was studied. Microcosms were incubated with 100 individuals of a fungus-feeding (Aphelenchus avenae) or a bacteria-feeding nematode species (Caenorhabditis elegans) respectively, and bacterial activity was determined after 0, 1, 2, 4, and 7 days. Significant time and feeding-type effects were found, with consistently higher bacterial activity estimates in treatments with bacteria-feeding nematodes. These results suggest that grazing affects bacterial activity, and indicate that grazing by nematodes may be more important in stimulating bacterial activity than bioturbation or excretion. Combining these results, we conclude that natural nematode communities may have an impact on bacterial activity, and that the magnitude of this impact depends on the proportion of actively feeding bactivores within the community. Received: 2 September 1996 / Accepted: 20 May 1997     

Bacterial mortality and the fate of bacterial production

Knowledge of the rates of bacterial mortality, particularly predatory mortality, is important in determining the fate of bacterial production. Communities of planktonic bacteria have specific growth rates on the order of 1 d⁻¹, but there is relatively little variation in bacterial abundance, implying that growth and mortality are closely coupled. A review of the mechanisms of bacterial mortality suggests that predation and parasitism are the most likely factors balancing the rapid rates of bacterial growth on daily time-scales. Experiments done in two-stage continuous cultures partially support this notion. At bacterial growth rates of 1 d⁻¹, predatory mortality was on the order of 1.5–2 d⁻¹ and nonpredatory mortality was undetectable. On the other hand, a review of existing field studies indicates that neither predation by metazoans nor protists balances rates of bacterial growth. Improved methods for measuring bacterial growth and mortality and studies of the nonpredatory mechanisms of bacterial mortality are required to resolve this paradox.     

Off the hook--how bacteria survive protozoan grazing

Bacterial growth and survival in numerous environments are constrained by the action of bacteria-consuming protozoa. Recent findings suggest that bacterial adaptations against protozoan predation might have a significant role in bacterial persistence and diversification. We argue that selective predation has given rise to diverse routes of bacterial defense, including adaptive mechanisms in bacterial biofilms, and has promoted major transitions in bacterial evolution, such as multicellularity and pathogenesis. We propose that studying predation-driven adaptations will provide an exciting frontier for microbial ecology and evolution at the interface of prokaryotes and eukaryotes.     

A small molecule that disrupts S. Typhimurium membrane voltage without cell lysis reduces bacterial colonization of mice

As pathogenic bacteria become increasingly resistant to antibiotics, antimicrobials with mechanisms of action distinct from current clinical antibiotics are needed. Gram-negative bacteria pose a particular problem because they defend themselves against chemicals with a minimally permeable outer membrane and with efflux pumps. During infection, innate immune defense molecules increase bacterial vulnerability to chemicals by permeabilizing the outer membrane and occupying efflux pumps. Therefore, screens for compounds that reduce bacterial colonization of mammalian cells have the potential to reveal unexplored therapeutic avenues. Here we describe a new small molecule, D66, that prevents the survival of a human Gram-negative pathogen in macrophages. D66 inhibits bacterial growth under conditions wherein the bacterial outer membrane or efflux pumps are compromised, but not in standard microbiological media. The compound disrupts voltage across the bacterial inner membrane at concentrations that do not permeabilize the inner membrane or lyse cells. Selection for bacterial clones resistant to D66 activity suggested that outer membrane integrity and efflux are the two major bacterial defense mechanisms against this compound. Treatment of mammalian cells with D66 does not permeabilize the mammalian cell membrane but does cause stress, as revealed by hyperpolarization of mitochondrial membranes. Nevertheless, the compound is tolerated in mice and reduces bacterial tissue load. These data suggest that the inner membrane could be a viable target for anti-Gram-negative antimicrobials, and that disruption of bacterial membrane voltage without lysis is sufficient to enable clearance from the host.     

Subcellular localization of RNA and proteins in prokaryotes

The field of bacterial cell biology has been revolutionized in the last decade by improvements in imaging capabilities which have revealed that bacterial cells, previously thought to be non-compartmentalized, possess an intricate higher-order organization. Many bacterial proteins localize to specific subcellular domains and regulate the spatial deployment of other proteins, DNA and lipids. Recently, the surprising discovery was made that bacterial RNA molecules are also specifically localized. However, the mechanisms that underlie bacterial cell architecture are just starting to be unraveled. The limited number of distribution patterns observed thus far for bacterial proteins and RNAs, and the similarity between the patterns exhibited by these macromolecules, suggest that the processes that underlie their localization are inextricably linked. We discuss these spatial arrangements and the insights that they provide on processes, such as localized translation, protein complex formation, and crosstalk between bacterial machineries.     

A new experimental approach for studying bacterial genomic island evolution identifies island genes with bacterial host-specific expression patterns

Background  

Genomic islands are regions of bacterial genomes that have been acquired by horizontal transfer and often contain blocks of genes that function together for specific processes. Recently, it has become clear that the impact of genomic islands on the evolution of different bacterial species is significant and represents a major force in establishing bacterial genomic variation. However, the study of genomic island evolution has been mostly performed at the sequence level using computer software or hybridization analysis to compare different bacterial genomic sequences. We describe here a novel experimental approach to study the evolution of species-specific bacterial genomic islands that identifies island genes that have evolved in such a way that they are differentially-expressed depending on the bacterial host background into which they are transferred.     

非编码小RNA对细菌毒力及耐药性的调控作用研究进展

近年来的研究发现,细菌非编码小RNA (small non-coding RNA, sRNA)对其不同生理进程起到了重要的调控作用。随着大量sRNA被发现并鉴定,细菌sRNA的功能被逐步阐明,其可在转录后水平广泛调控细菌的生理代谢、毒力及耐药性等。本文综述了sRNA对细菌毒力和耐药性调控作用的研究进展,对揭示细菌转录后水平毒力及耐药性调控机制具有一定意义。     

Low root functional dispersion enhances functionality of plant growth by influencing bacterial activities in European forest soils

Current studies show that multispecies forests are beneficial regarding biodiversity and ecosystem functionality. However, there are only little efforts to understand the ecological mechanisms behind these advantages of multispecies forests. Bacteria are among the key plant growth-promoting microorganisms that support tree growth and fitness. Thus, we investigated links between bacterial communities, their functionality and root trait dispersion within four major European forest types comprising multispecies and monospecific plots. Bacterial diversity revealed no major changes across the root functional dispersion gradient. In contrast, predicted gene profiles linked to plant growth activities suggest an increasing bacterial functionality from monospecific to multispecies forest. In multispecies forest plots, the bacterial functionality linked to plant growth activities declined with the increasing functional dispersion of the roots. Our findings indicate that enriched abundant bacterial operational taxonomic units are decoupled from bacterial functionality. We also found direct effects of tree species identity on bacterial community composition but no significant relations with root functional dispersion. Additionally, bacterial network analyses indicated that multispecies forests have a higher complexity in their bacterial communities, which points towards more stable forest systems with greater functionality. We identified a potential of root dispersion to facilitate bacterial interactions and consequently, plant growth activities.     

水生细菌生物量的估算方法*

细菌的生物量是海洋微生物研究的关键参数之一。目前,细菌生物量估算方法主要根据其体积的大小进行换算,但换算的方式也不尽一致。对细菌体积和细菌碳含量主要的测定方法、体积与生物量之间换算系数、换算模式进行介绍,评述。认为流式细胞术是测定细菌体积较为合适的方法,X-射线微量分析法是测定单个细菌生物量(碳含量)最合适的方法,异速生长模式是目前生物量换算过程较为常用的模式。     

Bacterial diversity in three distinct sub-habitats within the pitchers of the northern pitcher plant, Sarracenia purpurea

Pitcher plants have been widely used in ecological studies of food webs; however, their bacterial communities are poorly characterized. Pitchers of Sarracenia purpurea contain several distinct sub-habitats, namely the bottom sediment, the liquid, and the internal pitcher wall. We hypothesized that those three sub-habitats within pitcher plants are inhabited by distinct bacterial populations. We used denaturing gradient gel electrophoresis and 16S rRNA gene sequencing to characterize bacterial populations in pitchers from three bogs. DGGE and sequencing revealed that in any given pitcher, the three sub-habitats contain significantly different bacterial populations. However, there was significant variability between bacterial populations inhabiting the same type of habitat in different pitchers, even at the same site. Therefore, no consistent set of bacterial populations was enriched in any of the three sub-habitats. All sub-habitats appeared to be dominated by alpha- and betaproteobacteria in differing proportions. In addition, sequences from the Bacteroidetes and Firmicutes were obtained from all three sub-habitats. We conclude that container aquatic habitats such as the pitchers of S.?purpurea possess a very high bacterial diversity, with many unique bacterial populations enriched in individual pitchers. Within an individual pitcher, populations of certain bacterial families may be enriched in one of the three studied sub-habitats.     

基于高通量测序技术的不同年代公园绿地土壤细菌多样性

【背景】细菌多样性对绿地土壤生态功能有重要作用,但不同年代公园绿地土壤的细菌多样性尚未见相关报道。【目的】研究北京市不同年代公园绿地土壤细菌多样性和群落结构特征。【方法】利用IlluminaMiSeq测序技术,分别对北京市代表性古典公园和现代公园绿地土壤细菌群落多样性进行分析。【结果】北京市公园绿地土壤细菌群落共划分为45个已知的菌门,其中变形菌门、酸杆菌门、绿弯菌门和放线菌门为优势细菌群。土壤细菌群落α多样性分析结果表明,古典公园和现代公园的土壤细菌多样性存在差异,表现为古典公园的丰富度和多样性都高于现代公园。此外,土壤细菌群落相似性分析和主坐标分析都表明古典公园和现代公园的土壤细菌群落结构存在显著差异。冗余分析表明,对土壤微生物群落结构产生显著影响的环境因子分别为土壤含水量、有机质和全氮,其它土壤环境因子无统计学意义。首次引入公园年代作为影响因子进行冗余分析的研究结果表明,公园年代为影响公园细菌群落多样性的重要因子。【结论】不同年代公园绿地土壤细菌群落结构和物种多样性具有显著差异,随着公园年代的增加,土壤肥力和微生物多样性增加,绿地生态系统更稳定,可通过制定不同的绿地管理措施改变公园绿地土壤环境,进而优化土壤细菌群落结构,促进土壤碳氮养分循环,提高土壤肥力。