Quantitative Metaproteomics and Activity-based Protein Profiling of Patient Fecal Microbiome Identifies Host and Microbial Serine-type Endopeptidase Activity Associated With Ulcerative Colitis

The gut microbiota plays an important yet incompletely understood role in the induction and propagation of ulcerative colitis (UC). Organism-level efforts to identify UC-associated microbes have revealed the importance of community structure, but less is known about the molecular effectors of disease. We performed 16S rRNA gene sequencing in parallel with label-free data-dependent LC-MS/MS proteomics to characterize the stool microbiomes of healthy (n = 8) and UC (n = 10) patients. Comparisons of taxonomic composition between techniques revealed major differences in community structure partially attributable to the additional detection of host, fungal, viral, and food peptides by metaproteomics. Differential expression analysis of metaproteomic data identified 176 significantly enriched protein groups between healthy and UC patients. Gene ontology analysis revealed several enriched functions with serine-type endopeptidase activity overrepresented in UC patients. Using a biotinylated fluorophosphonate probe and streptavidin-based enrichment, we show that serine endopeptidases are active in patient fecal samples and that additional putative serine hydrolases are detectable by this approach compared with unenriched profiling. Finally, as metaproteomic databases expand, they are expected to asymptotically approach completeness. Using ComPIL and de novo peptide sequencing, we estimate the size of the probable peptide space unidentified (“dark peptidome”) by our large database approach to establish a rough benchmark for database sufficiency. Despite high variability inherent in patient samples, our analysis yielded a catalog of differentially enriched proteins between healthy and UC fecal proteomes. This catalog provides a clinically relevant jumping-off point for further molecular-level studies aimed at identifying the microbial underpinnings of UC.     

Species turnover in ant assemblages is greater horizontally than vertically in the world's tallest tropical forest

Abiotic and biotic factors structure species assembly in ecosystems both horizontally and vertically. However, the way community composition changes along comparable horizontal and vertical distances in complex three‐dimensional habitats, and the factors driving these patterns, remains poorly understood. By sampling ant assemblages at comparable vertical and horizontal spatial scales in a tropical rainforest, we tested hypotheses that predicted differences in vertical and horizontal turnover explained by different drivers in vertical and horizontal space. These drivers included environmental filtering, such as microclimate (temperature, humidity, and photosynthetic photon flux density) and microhabitat connectivity (leaf area), which are structured differently across vertical and horizontal space. We found that both ant abundance and richness decreased significantly with increasing vertical height. Although the dissimilarity between ant assemblages increased with vertical distance, indicating a clear distance‐decay pattern, the dissimilarity was higher horizontally where it appeared independent of distance. The pronounced horizontal and vertical structuring of ant assemblages across short distances is likely explained by a combination of microclimate and microhabitat connectivity. Our results demonstrate the importance of considering three‐dimensional spatial variation in local assemblages and reveal how highly diverse communities can be supported by complex habitats.     

How does landscape context contribute to effects of habitat fragmentation on diversity and population density of butterflies?

Aim Studies on habitat fragmentation of insect communities mostly ignore the impact of the surrounding landscape matrix and treat all species equally. In our study, on habitat fragmentation and the importance of landscape context, we expected that habitat specialists are more affected by area and isolation, and habitat generalists more by landscape context. Location and methods The study was conducted in the vicinity of the city of Göttingen in Germany in the year 2000. We analysed butterfly communities by transect counts on thirty‐two calcareous grasslands differing in size (0.03–5.14 ha), isolation index (2100–86,000/edge‐to‐edge distance 55–1894 m), and landscape diversity (Shannon–Wiener: 0.09–1.56), which is correlated to percentage grassland in the landscape. Results A total of 15,185 butterfly specimens belonging to fifty‐four species are recorded. In multiple regression analysis, the number of habitat specialist (n = 20) and habitat generalist (n = 34) butterfly species increased with habitat area, but z‐values (slopes) of the species–area relationships for specialists (z = 0.399) were significantly steeper compared with generalists (z = 0.096). Generalists, but not specialists, showed a marginally significant increase with landscape diversity. Effects of landscape diversity were scale‐dependent and significant only at the smallest scale (landscape context within a 250 m radius around the habitat). Habitat isolation was not related to specialist and generalist species numbers. In multiple regression analysis the density of specialists increased significantly with habitat area, whereas generalist density increased only marginally. Habitat isolation and landscape diversity did not show any effects. Main conclusions Habitat area was the most important predictor of butterfly community structure and influenced habitat specialists more than habitat generalists. In contrast to our expectations, habitat isolation had no effect as most butterflies could cope with the degree of isolation in our study region. Landscape diversity appeared to be important for generalist butterflies only.     

Coral reef mesopredators switch prey,shortening food chains,in response to habitat degradation

Diet specificity is likely to be the key predictor of a predator's vulnerability to changing habitat and prey conditions. Understanding the degree to which predatory coral reef fishes adjust or maintain prey choice, in response to declines in coral cover and changes in prey availability, is critical for predicting how they may respond to reef habitat degradation. Here, we use stable isotope analyses to characterize the trophic structure of predator–prey interactions on coral reefs of the Keppel Island Group on the southern Great Barrier Reef, Australia. These reefs, previously typified by exceptionally high coral cover, have recently lost much of their coral cover due to coral bleaching and frequent inundation by sediment‐laden, freshwater flood plumes associated with increased rainfall patterns. Long‐term monitoring of these reefs demonstrates that, as coral cover declined, there has been a decrease in prey biomass, and a shift in dominant prey species from pelagic plankton‐feeding damselfishes to territorial benthic algal‐feeding damselfishes, resulting in differences in the principal carbon pathways in the food web. Using isotopes, we tested whether this changing prey availability could be detected in the diet of a mesopredator (coral grouper, Plectropomus maculatus). The δ¹³C signature in grouper tissue in the Keppel Islands shifted from a more pelagic to a more benthic signal, demonstrating a change in carbon sources aligning with the change in prey availability due to habitat degradation. Grouper with a more benthic carbon signature were also feeding at a lower trophic level, indicating a shortening in food chains. Further, we found a decline in the coral grouper population accompanying a decrease in total available prey biomass. Thus, while the ability to adapt diets could ameliorate the short‐term impacts of habitat degradation on mesopredators, long‐term effects may negatively impact mesopredator populations and alter the trophic structure of coral reef food webs.     

唐家河自然保护区大熊猫种群数量及栖息地的移动

本文根据大熊猫季节性活动规律特点,应用海拔高度路线调查法,全面收集唐家河自然保护区大熊猫的比较新鲜粪便,计获１２４个粪样材料,提取ＤＮＡ作ＤＮＡ指纹图,经微机检测,保护区有大熊猫３７只,个体数量与粪样采集量之比为１∶３３５１４,有６个家系,雌兽２１只,雄兽１６只。并搞清了保护区生态环境质量,箭竹遭受病虫害的程度,洪水对栖息地的影响,特别对引起大熊猫数量减少及栖息地移动等原因,作了较为详细的分析。     

Island biogeography of temporary wetland carabid beetle communities

Aim The study tests if island biogeography is applicable to invertebrate communities of habitat islands in the agricultural landscape that are not fragments of formerly larger habitats. Location Thirty temporary wetlands in the agricultural landscape of northeast Germany. Methods The composition and species richness of carabid beetle communities was analysed. Habitat area, isolation, the density of temporary wetlands in the landscape, land‐use intensity and the maximum duration of flooding were recorded as independent variables. Overall species richness and wetland species richness were studied in independent regression analyses. The community composition was analysed by means of a Canonical Correspondence Analysis (CCA). A partial CCA was used to analyse the effect of the distance to the edge of the field after removing impacts of other independent variables. Results The area of the habitats and various measures of isolation (mean distances = 81–240 m) did not influence species richness or wetland species richness. The community composition was mainly determined by the land‐use intensity, habitat area did not have significant effects, and the distance to the edge of the field was the only effective isolation parameter. Short‐winged species were more often affected by the distance to the edge of the field than full‐winged species. Main conclusion There is evidence that the distances between the wetlands do not provide an effective barrier to the species dispersal and, therefore, metapopulation structures including subpopulations of multiple temporary wetlands might counteract local area effects on subpopulations. Short‐winged species, however, might be more affected by isolation than full‐winged species. As carabid beetle community structure in most early successional habitats is similar, these results may be representative of many agricultural landscape habitats. Nature conservancy concepts that aim to increase habitat area and habitat connectivity have successfully been applied to fragmented late‐successional habitats. The present study indicates that such concepts do not necessarily result in higher diversity or larger populations in early successional habitats.     

不同鸟类生境网络复合与优化——以苏锡常地区白鹭、鸳鸯、雉鸡为例

通过复合优化不同焦点物种的生境网络表征多数物种生境网络实现物种多样性保护,具有重要理论价值和实践意义。以苏锡常地区为研究区域,以白鹭、鸳鸯和雉鸡3种鸟类为焦点物种,通过采用生境斑块约束条件模型与最小成本路径法相结合的方法识别出生境网络;从满足集合覆盖问题视角出发,通过采用网络构成要素复合的方法进行网络复合,其中廊道与廊道的复合通过采用评价生态系统服务价值的方法实现;通过采用观测数据为生境斑块和迁移廊道增补依据的方法进行复合生境网络优化。结果表明:生境网络经过复合,廊道总面积、总长度及生态系统服务价值在分别减少了16%、68%和10%的情况下,保持了斑块间的连接度、兼顾到经济效益和生态效益最大化、覆盖了占总数86%以上的75处观测点;复合生境网络经过优化,覆盖了2010年及以后所有84处观测点,廊道总面积、总长度及生态系统服务价值分别增加了19%、21%和27%;说明生境网络复合优化定量分析方法和思路具有可行性,为网络复合研究提供了借鉴。