Genomic changes underlying host specialization in the bee gut symbiont Lactobacillus Firm5

Bacteria that engage in long‐standing associations with particular hosts are expected to evolve host‐specific adaptations that limit their capacity to thrive in other environments. Consistent with this, many gut symbionts seem to have a limited host range, based on community profiling and phylogenomics. However, few studies have experimentally investigated host specialization of gut symbionts and the underlying mechanisms have largely remained elusive. Here, we studied host specialization of a dominant gut symbiont of social bees, Lactobacillus Firm5. We show that Firm5 strains isolated from honey bees and bumble bees separate into deep‐branching host‐specific phylogenetic lineages. Despite their divergent evolution, colonization experiments show that bumble bee strains are capable of colonizing the honey bee gut. However, they were less successful than honey bee strains, and competition with honey bee strains completely abolished their colonization. In contrast, honey bee strains of divergent phylogenetic lineages were able to coexist within individual bees. This suggests that both host selection and interbacterial competition play important roles in host specialization. Using comparative genomics of 27 Firm5 isolates, we found that the genomes of honey bee strains harbour more carbohydrate‐related functions than bumble bee strains, possibly providing a competitive advantage in the honey bee gut. Remarkably, most of the genes encoding carbohydrate‐related functions were not conserved among the honey bee strains, which suggests that honey bees can support a metabolically more diverse community of Firm5 strains than bumble bees. These findings advance our understanding of the genomic changes underlying host specialization.     

Toward molecular trait‐based ecology through integration of biogeochemical,geographical and metagenomic data

Using metagenomic ‘parts lists’ to infer global patterns on microbial ecology remains a significant challenge. To deduce important ecological indicators such as environmental adaptation, molecular trait dispersal, diversity variation and primary production from the gene pool of an ecosystem, we integrated 25 ocean metagenomes with geographical, meteorological and geophysicochemical data. We find that climatic factors (temperature, sunlight) are the major determinants of the biomolecular repertoire of each sample and the main limiting factor on functional trait dispersal (absence of biogeographic provincialism). Molecular functional richness and diversity show a distinct latitudinal gradient peaking at 20°N and correlate with primary production. The latter can also be predicted from the molecular functional composition of an environmental sample. Together, our results show that the functional community composition derived from metagenomes is an important quantitative readout for molecular trait‐based biogeography and ecology.     

人体肠道宏基因组生物信息分析方法

最近5年来,微生物组与人体健康之间的微妙关系已成为全球研究热点,特别是基于高通量测序的宏基因组技术推动了这个领域的发展。然而宏基因组生物信息学分析往往是开展研究过程中的难点。本文对宏基因组生物信息常规分析方法进行了介绍。     

High‐throughput metabarcoding of eukaryotic diversity for environmental monitoring of offshore oil‐drilling activities

As global exploitation of available resources increases, operations extend towards sensitive and previously protected ecosystems. It is important to monitor such areas in order to detect, understand and remediate environmental responses to stressors. The natural heterogeneity and complexity of communities means that accurate monitoring requires high resolution, both temporally and spatially, as well as more complete assessments of taxa. Increased resolution and taxonomic coverage is economically challenging using current microscopy‐based monitoring practices. Alternatively, DNA sequencing‐based methods have been suggested for cost‐efficient monitoring, offering additional insights into ecosystem function and disturbance. Here, we applied DNA metabarcoding of eukaryotic communities in marine sediments, in areas of offshore drilling on the Norwegian continental shelf. Forty‐five samples, collected from seven drilling sites in the Troll/Oseberg region, were assessed, using the small subunit ribosomal RNA gene as a taxonomic marker. In agreement with results based on classical morphology‐based monitoring, we were able to identify changes in sediment communities surrounding oil platforms. In addition to overall changes in community structure, we identified several potential indicator taxa, responding to pollutants associated with drilling fluids. These included the metazoan orders Macrodasyida, Macrostomida and Ceriantharia, as well as several ciliates and other protist taxa, typically not targeted by environmental monitoring programmes. Analysis of a co‐occurrence network to study the distribution of taxa across samples provided a framework for better understanding the impact of anthropogenic activities on the benthic food web, generating novel, testable hypotheses of trophic interactions structuring benthic communities.     

Targeted metagenomics reveals extensive diversity of the denitrifying community in partial nitritation anammox and activated sludge systems

The substantial presence of denitrifiers has already been reported in partial nitritation anammox (PNA) systems using the 16S ribosomal RNA (rRNA) gene, but little is known about the phylogenetic diversity based on denitrification pathway functional genes. Therefore, we performed a metagenomic analysis to determine the distribution of denitrification genes and the associated phylogeny in PNA systems and whether a niche separation between PNA and conventional activated sludge (AS) systems exists. The results revealed a distinct abundance pattern of denitrification pathway genes and their association to the microbial species between PNA and AS systems. In contrast, the taxonomic analysis, based on the 16S rRNA gene, did not detect notable variability in denitrifying community composition across samples. In general, narG and nosZa2 genes were dominant in all samples. While the potential for different stages of denitrification was redundant, variation in species composition and lack of the complete denitrification gene pool in each species appears to confer niche separation between PNA and AS systems. This study suggests that targeted metagenomics can help to determine the denitrifying microbial composition at a fine‐scale resolution while overcoming current biases in quantitative polymerase chain reaction approaches due to a lack of appropriate primers.     

The community ecology of pathogens: coinfection,coexistence and community composition

Disease and community ecology share conceptual and theoretical lineages, and there has been a resurgence of interest in strengthening links between these fields. Building on recent syntheses focused on the effects of host community composition on single pathogen systems, we examine pathogen (microparasite) communities using a stochastic metacommunity model as a starting point to bridge community and disease ecology perspectives. Such models incorporate the effects of core community processes, such as ecological drift, selection and dispersal, but have not been extended to incorporate host–pathogen interactions, such as immunosuppression or synergistic mortality, that are central to disease ecology. We use a two‐pathogen susceptible‐infected (SI) model to fill these gaps in the metacommunity approach; however, SI models can be intractable for examining species‐diverse, spatially structured systems. By placing disease into a framework developed for community ecology, our synthesis highlights areas ripe for progress, including a theoretical framework that incorporates host dynamics, spatial structuring and evolutionary processes, as well as the data needed to test the predictions of such a model. Our synthesis points the way for this framework and demonstrates that a deeper understanding of pathogen community dynamics will emerge from approaches working at the interface of disease and community ecology.     

Phylogenetic community ecology of soil biodiversity using mitochondrial metagenomics

High‐throughput DNA methods hold great promise for the study of taxonomically intractable mesofauna of the soil. Here, we assess species diversity and community structure in a phylogenetic framework, by sequencing total DNA from bulk specimen samples and assembly of mitochondrial genomes. The combination of mitochondrial metagenomics and DNA barcode sequencing of 1494 specimens in 69 soil samples from three geographic regions in southern Iberia revealed >300 species of soil Coleoptera (beetles) from a broad spectrum of phylogenetic lineages. A set of 214 mitochondrial sequences longer than 3000 bp was generated and used to estimate a well‐supported phylogenetic tree of the order Coleoptera. Shorter sequences, including cox1 barcodes, were placed on this mitogenomic tree. Raw Illumina reads were mapped against all available sequences to test for species present in local samples. This approach simultaneously established the species richness, phylogenetic composition and community turnover at species and phylogenetic levels. We find a strong signature of vertical structuring in soil fauna that shows high local community differentiation between deep soil and superficial horizons at phylogenetic levels. Within the two vertical layers, turnover among regions was primarily at the tip (species) level and was stronger in the deep soil than leaf litter communities, pointing to layer‐mediated drivers determining species diversification, spatial structure and evolutionary assembly of soil communities. This integrated phylogenetic framework opens the application of phylogenetic community ecology to the mesofauna of the soil, among the most diverse and least well‐understood ecosystems, and will propel both theoretical and applied soil science.     

沈阳地区稻田节肢动物群落结构及群落生态研究

通过对沈阳地区稻田生态系统节肢动物群落结构及群落生态研究。共查得。属昆虫纲的有10个目的29科66种,其中天敌昆虫种类有7目20科51种,属蜘蛛纲的有蜘蛛目10科20种。用空间及时间生态位分析了害虫与天敌两个营养阶层间的关系。稻田生态系统节肢动物的多样性指数、均匀度与优势度分析表明,各类群落受外界干扰都很敏感,且表现一致性。依据节肢动物群落的结构及规律,结合沈阳地区水稻生长、栽培条件,用最优分割方法将稻田群落分为4个阶段,并提出了不同阶段害虫群落特点及害虫防治对策。     

Environmental monitoring through protist next‐generation sequencing metabarcoding: assessing the impact of fish farming on benthic foraminifera communities

The measurement of species diversity represents a powerful tool for assessing the impacts of human activities on marine ecosystems. Traditionally, the impact of fish farming on the coastal environment is evaluated by monitoring the dynamics of macrobenthic infaunal populations. However, taxonomic sorting and morphology‐based identification of the macrobenthos demand highly trained specialists and are extremely time‐consuming and costly, making it unsuitable for large‐scale biomonitoring efforts involving numerous samples. Here, we propose to alleviate this laborious task by developing protist metabarcoding tools based on next‐generation sequencing (NGS) of environmental DNA and RNA extracted from sediment samples. In this study, we analysed the response of benthic foraminiferal communities to the variation of environmental gradients associated with salmon farms in Scotland. We investigated the foraminiferal diversity based on ribosomal minibarcode sequences generated by the Illumina NGS technology. We compared the molecular data with morphospecies counts and with environmental gradients, including distance to cages and redox used as a proxy for sediment oxygenation. Our study revealed high variations between foraminiferal communities collected in the vicinity of fish farms and at distant locations. We found evidence for species richness decrease in impacted sites, especially visible in the RNA data. We also detected some candidate bioindicator foraminiferal species. Based on this proof‐of‐concept study, we conclude that NGS metabarcoding using foraminifera and other protists has potential to become a new tool for surveying the impact of aquaculture and other industrial activities in the marine environment.     

Geographical ecology of Paraguayan bats: spatial integration and metacommunity structure of interacting assemblages

We examined the relative contributions of regional spatial characteristics and local environmental conditions in determining Paraguayan bat species composition. We used a suite of full and partial redundancy analyses to estimate four additive partitions of variance in bat species composition: (a) unexplained variation, (b) that explained purely by spatial characteristics, (c) that explained purely by local environmental conditions and (d) that explained jointly by space and environment. The spatial component to bat species composition was greater than the environmental component and both pure spatial and pure environmental characteristics accounted for significant amounts of variation in bat species composition. Results from variance decomposition suggest that the mass effects model describes metacommunity structure of Paraguayan bats better than species sorting or neutral models. Such mass effects may potentially be general for bats and could explain the inability of purely local factors to fully account for bat community organization. Mass effects also have substantial conservation implications because rescue effects may enhance the persistence of mobile species in fragmented landscapes with relatively few protected sites.     

泉州湾大型底栖生物群落生态

泉州湾大型底栖生物有256种,其中多毛类66种,软体动物74种,甲壳动物77种,棘皮动物12种和其他动物27种。多毛类、软体动物和甲壳动物占总种数的84．76％。三者构成大型底栖生物的主要类群。春季、夏季、秋季和冬季4个季节平均生物量为23．13g/m^2,平均栖息密度为144个／m^2。数量组成,生物量以软体动物居首位10．28g/m^2,棘皮动物居第二位5．44g／m^2;栖息密度以软体动物占第一位78个／m^2,多毛类占第二位37个／m^2。泉州湾大型底栖生物主要有2个群落：群落Ⅰ。丝鳃稚齿虫一光滑河篮蛤-纹尾长眼虾群落;群落Ⅱ,中蚓虫-光滑河篮蛤-模糊新短眼蟹群落。泉州湾大型底栖生物群落出现一定扰动,主要在于群落的季节演替。     

Comparison of microbial community assays for the assessment of stream biofilm ecology

We investigated a range of microbiological community assays performed on scrapes of biofilms formed on artificial diffusing substrates deployed in 8 streams in eastern Scotland, with a view to using them to characterize ecological response to stream water quality. The assays considered were: Multiplex Terminal Restriction Fragment Length Polymorphism or M-TRFLP (a molecular method), Phospholipid Fatty Acid or PLFA analysis (a biochemical method) and MICRORESP^™ (a physiological method) alongside TDI, diatom species, and chlorophyll a content. Four of the streams were classified as of excellent status (3-6 μg/L Soluble Reactive Phosphorus (SRP)) with respect to soluble P content under the EU Water Framework Directive and four were of borderline good/moderate or moderate status (43-577 μg/L SRP). At each site, 3 replicates of 3 solute diffusion treatments were deployed in a Latin square design. Solute diffusion treatments were: KCl (as a control solute), N and P (to investigate the effect of nutrient enrichment), or the herbicide isoproturon (as a “high impact” control, which aimed to affect biofilm growth in a way detectable by all assays). Biofilms were sampled after 4 weeks deployment in a low flow period of early summer 2006.The chlorophyll a content of biofilms after 4 weeks was 2.0 ± 0.29 mg/m² (mean ± se). Dry matter content was 16.0 ± 13.1 g/m². The M-TRFLP was successfully used for generating community profiles of cyanobacteria, algae and bacteria and was much faster than diatom identification. The PFLA and TDI were successful after an increase in the sample size, due to low counts. The MICRORESP^™ assays were often below or near detection limit. We estimated the per-sample times for the successful assays as follows: M-TRFLP: 20 min, PLFA 40 min, TDI 90 min. Using MANOVA on the first 5 principal co-ordinates, all the assays except MICRORESP^™ showed significant differences between sites, but none of the assays showed a significant effect of either initial stream trophic status (as classified by the EU Water Framework Directive using chemical standards for soluble P), or of the diffusing solute treatment. Multiple Procrustes analysis on the ordination results showed that the diatom and M-TRFLP data sets hold distinct, though as yet unexplored, information about the ecological factors affecting stream biofilms. The diatom data were subjected to principal components analysis, to identify which taxa were more strongly influenced by site variables, trophic status or treatment effects. These were Acnanthes lanceolata, A. minutissimma, Nitzchia spp., Coccineis spp. and Navicula spp. Further experimentation and data analysis on a larger number of sites, to identify specific M-TRFLP bands that could be used as indicators linked to specific taxa, are desirable. Results highlight the need for a multifactorial approach to understanding controls on stream ecology.     

The historic biogeography and community ecology of Polynesian pigeons and doves

The species richness, taxonomic diversity, and geographic distribution of pigeons and doves (Columbidae) have been altered irreversibly in Polynesia by 3500 years of human activity. Natural (without human influence) columbid faunas are estimated primarily by studying prehistoric bones. In all Polynesian island groups studied (except outlying Easter Island, Hawaiian Islands, or New Zealand), the prehistoric columbid faunas had more species, more genera, and more species per genus than modern faunas from the same island. Congeneric species pairs or triplets occurred on many islands for Ducula , Ptilinopus , and Gallicolumba. The losses of Polynesian columbids include the extinction of at least 9 species in the genera Ducula , Ptilinopus , Macropygia , Caloenas , Gallicolumba , and Didunculus as well as the extirpation of numerous island populations of extant species. If not for human impact, a typical East Polynesian island would support at least 5–6 species of columbids in 3–4 genera (compared to 0–3 species in 0–3 genera today). A typical West Polynesian island would support at least 6–7 species in 4–5 genera (compared to 1–6 species in 1–5 genera today). Since all Polynesian pigeons and doves are frugivorous and/or granivorous, their decline in recent millennia probably has affected the composition of Polynesian forests by limiting inter- and intra-island dispersal of plant propagules.     

Eco-evolutionary feedbacks in community and ecosystem ecology: interactions between the ecological theatre and the evolutionary play

Interactions between natural selection and environmental change are well recognized and sit at the core of ecology and evolutionary biology. Reciprocal interactions between ecology and evolution, eco-evolutionary feedbacks, are less well studied, even though they may be critical for understanding the evolution of biological diversity, the structure of communities and the function of ecosystems. Eco-evolutionary feedbacks require that populations alter their environment (niche construction) and that those changes in the environment feed back to influence the subsequent evolution of the population. There is strong evidence that organisms influence their environment through predation, nutrient excretion and habitat modification, and that populations evolve in response to changes in their environment at time-scales congruent with ecological change (contemporary evolution). Here, we outline how the niche construction and contemporary evolution interact to alter the direction of evolution and the structure and function of communities and ecosystems. We then present five empirical systems that highlight important characteristics of eco-evolutionary feedbacks: rotifer–algae chemostats; alewife–zooplankton interactions in lakes; guppy life-history evolution and nutrient cycling in streams; avian seed predators and plants; and tree leaf chemistry and soil processes. The alewife–zooplankton system provides the most complete evidence for eco-evolutionary feedbacks, but other systems highlight the potential for eco-evolutionary feedbacks in a wide variety of natural systems.     

Bridging the gap between community ecology and historical biogeography: niche conservatism and community structure in emydid turtles

Historical (phylogenetic) biogeography and community ecology were once integrated as part of the broader study of organismal diversity, but in recent decades have become largely separate disciplines. This is unfortunate because many patterns studied by community ecologists may originate through processes studied by historical biogeographers and vice versa. In this study, we explore the causes of a geographic pattern of community structure (habitat use) in the emydid turtle assemblages of eastern North America, with more semi-terrestrial species of the subfamily Emydinae in the north and more aquatic species of Deirochelyinae in the south. Specifically, we address the factors that prevent northern emydines from invading southern communities. We test for competitive exclusion by examining patterns of range overlap, and test for the role of niche conservatism using analyses of climatic and physiological data based on a multilocus molecular phylogeny. We find no support for competitive exclusion, whereas several lines of evidence support the idea that niche conservatism has prevented northern emydines from dispersing into southern communities. Our results show how understanding the causes of patterns of historical biogeography may help explain patterns of community structure.     

Stability of the gorilla microbiome despite simian immunodeficiency virus infection

Simian immunodeficiency viruses (SIVs) have been discovered in over 45 primate species; however, the pathogenic potential of most SIV strains remains unknown due to difficulties inherent in observing wild populations. Because those SIV infections that are pathogenic have been shown to induce changes in the host's gut microbiome, monitoring the microbiota present in faecal samples can provide a noninvasive means for studying the effects of SIV infection on the health of wild‐living primates. Here, we examine the effects of SIVgor, a close relative of SIVcpz of chimpanzees and HIV‐1 of humans, on the gut bacterial communities residing within wild gorillas, revealing that gorilla gut microbiomes are exceptionally robust to SIV infection. In contrast to the microbiomes of HIV‐1‐infected humans and SIVcpz‐infected chimpanzees, SIVgor‐infected gorilla microbiomes exhibit neither rises in the frequencies of opportunistic pathogens nor elevated rates of microbial turnover within individual hosts. Regardless of SIV infection status, gorilla microbiomes assort into enterotypes, one of which is compositionally analogous to those identified in humans and chimpanzees. The other gorilla enterotype appears specialized for a leaf‐based diet and is enriched in environmentally derived bacterial genera. We hypothesize that the acquisition of this gorilla‐specific enterotype was enabled by lowered immune system control over the composition of the microbiome. Our results indicate differences between the pathology of SIVgor and SIVcpz/HIV‐1 infections, demonstrating the utility of investigating host microbial ecology as a means for studying disease in wild primates of high conservation priority.     

鲻鱼(Mugil cephalus)寄生蠕虫群落生态研究

从1017尾鲻鱼（Mugil cephalus）肠道内获得寄生蠕虫9种,均为常见种类,即复殖吸虫（Digeneans）8种,棘头虫（Aacnthodephala）1种,总感染率为24.0％,平均感染强度8.73,种群平均密度2.10,其中惠东拟囊腔吸虫（Saccocoe-lioides huidongensis）的感染率、感染强度和平均密度最大。鲻鱼寄生蠕虫群落多样性指数为20193,群落均匀度指标为0.6370。鲻鱼感染寄生蠕虫种数在1－3种之间,优势种1种,为惠东拟腔吸虫;次优势种3种,分别为鲻长尾吸虫（E－longinus mugilus）、单睾椭囊吸虫（Elliptobursa singlorchis）和圆颚针鱼新棘吻虫（Neoechinorhynchus tylosuri）;非优势种5种,分别为楔形单脏吸虫（Haplosplanchnus cuneatus）、长形单脏吸虫（Haplosplanchnus elongatus）、双睾原单脏吸虫（Pro-haplosplanchus diorchis）、粤东纵睾吸虫（Tandemorchis yuedongensis）和浦里单脏吸虫（Haplosplanchnus purii）。略多于 寄生蠕虫复合群落和组分群落在一年四季中均由9种蠕虫组成,其感染率、平均感染强度和平均密度变化各有所不同,即从夏季开始,鲻鱼寄生蠕虫总感染率和各组分群落的平均密度则逐渐增高,冬季碹以一个高峰,随后逐渐下降;鲻鱼寄生蠕虫复合群落的平均密度从冬季开始逐渐下降,至秋季为最低;而圆颚针鱼析棘吻虫的感染率的四季变化与8种吸虫的变化趋势差异较大,即从春末开始增大,夏季达到最大值,随后维持在一个较高水平上,至春初则有所下降。9种寄生蠕虫的种间协调关系经卡方值测定,呈无明显协调关系。各种寄生蠕虫的种群分布均为聚集分布。