Composition and Similarity of Bovine Rumen Microbiota across Individual Animals

PDF HTML阅读 XML下载 导出引用 引用提醒 尖峰岭热带天然林不同土层细菌群落多样性和组成的海拔变异规律 DOI: 10.5846/stxb202203090570 作者: 作者单位: 作者简介: 通讯作者: 中图分类号: 基金项目: 国家自然科学基金项目（32171643，U1703332） The altitudinal patterns of bacterial community diversity and composition at different soil depths in Jianfengling mountain tropical forest Author: Affiliation: Fund Project: The National Natural Science Foundation of China (General Program, Key Program, Major Research Plan) 摘要 | 图/表 | 访问统计 | 参考文献 | 相似文献 | 引证文献 | 资源附件 | 文章评论 摘要:土壤微生物群落结构沿海拔梯度的变异是微生物生物地理学分异和群落空间分布的重要内容，然而，热带森林土壤微生物多样性及其群落特征的海拔模式尚不明确。研究海南省尖峰岭自然保护区0-20cm和20-40cm土壤细菌多样性和群落组成沿海拔梯度（400-1410m）的变化及其与环境因子的关系。结果表明：在0-20cm土壤微生物生物量碳、生物量氮和生物量磷随海拔升高（峰顶降低）而增加，20-40cm土壤微生物生物量碳、生物量氮和生物量磷随海拔升高呈先升高后降低趋势；整体上，变形菌门、放线菌门、酸杆菌门、拟杆菌门、厚壁菌门在0-20cm中占优势，丰度总和占该层细菌总量的88.17%；变形菌门、放线菌门、酸杆菌门、厚壁菌门、绿弯菌门在20-40cm中占优势，丰度总和占该层细菌总量的90.82%；随海拔增加，0-20cm细菌多样性线性减少，20-40cm细菌多样性变化不显著；沿海拔梯度，0-20cm细菌群落组成可分为低（409-1018m），中（1018-1357m）和高（1410m）三个海拔聚集群落，20-40cm细菌群落组成随海拔无显著性变化；两土层细菌多样性与土壤pH显著正相关，土壤细菌群落组成在0-20cm主要受年均温度和pH影响，20-40cm受年均温度和土壤有机碳影响；根据Bray-Curtis指数，0-20cm和20-40cm土壤细菌相似性随地理距离的增加逐渐降低，细菌群落相似性随环境距离的增大也逐渐降低。总之，尖峰岭土壤细菌多样性和群落组成的海拔格局受土壤深度影响，且驱动细菌群落组成变化的因素在土层间不同，暗示在未来气候变化背景下，热带森林0-20cm和20-40cm土壤微生物群落可能具有不同的响应机制。 Abstract:The variation of soil microbial community structure along the altitudinal gradient is an important content of microbial biogeographic differentiation and community spatial distribution. However, the altitudinal pattern of soil microbial diversity and its community characteristics in tropical forests is not clear. This paper studied the changes of bacterial diversity and community composition and their relationship with environmental factors in 0-20cm and 20-40cm soil depths along the altitudinal gradient (400-1410 m) in Jianfengling Nature Reserve, Hainan Province. The results showed that the soil microbial biomass carbon, biomass nitrogen and biomass phosphorus increased with the elevation of 0-20cm (the peak decreased), and the soil microbial biomass carbon, biomass nitrogen and biomass phosphorus increased first and then decreased with the elevation of 20-40cm. On the whole, Proteobacteria, Actinomycetes, Acidobacteria, Bacteroidetes and Firmicutes are dominant in 0-20cm, and the total abundance accounts for 88.17% of the total bacteria in this layer; Proteobacteria, Actinomycetes, Acidobacteria, Firmicutes and Chloroflexi are dominant in 20-40cm, and the total abundance accounts for 90.82% of the total bacteria in this layer. With the increase of altitude, the bacterial diversity decreased linearly in 0-20cm, and that of 20-40cm did not change significantly. The bacterial community composition of 0-20cm can be divided into three communities at low altitude (409-1018 m), medium altitude (1018-1357 m), and high altitude (1410 m) and the bacterial community composition of 20-40cm has no significant change with altitude. There was a significantly positive correlation between bacterial diversity and soil pH in the two soil depths. The composition of soil bacterial community was mainly affected by mean annual temperature and pH at 0-20cm, and by mean annual temperature and soil organic carbon at 20-40cm. According to the Bray Curtis index, the similarity of bacteria in 0-20cm and 20-40cm soil depths decreased with the increase of geographical distance, and the similarity of bacterial community also decreased with the increase of environmental distance. In a word, the altitudinal pattern of soil bacterial diversity and community composition in Jianfengling is affected by soil depth, and the factors driving the change of bacterial community composition are different among soil depths. It is suggested that the soil microbial communities in 0-20cm and 20-40cm of tropical forests may have different response mechanisms under the background of future climate change. 参考文献 相似文献 引证文献

AME Aquatic Microbial Ecology Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsSpecials AME 59:185-195 (2010) - DOI: https://doi.org/10.3354/ame01393 Spatial patterns of bacterial abundance, activity and community composition in relation to water masses in the eastern Mediterranean Sea Taichi Yokokawa1,*, Daniele De Corte1,2, Eva Sintes3, Gerhard J. Herndl1,3 1Department of Biological Oceanography, Royal Netherlands Institute for Sea Research (NIOZ), PO Box 59, 1790 AB, Den Burg, The Netherlands 2Center for Ecological and Evolutionary Studies, University of Groningen, PO Box 14, 9750 AA Haren, The Netherlands 3University of Vienna, Department of Marine Biology, Faculty Center of Ecology, Althanstrasse 14, 1090 Vienna, Austria *Email: taichi.yokokawa@nioz.nl ABSTRACT: To determine the variation of bacterial activity and community composition between and within specific water masses, samples were collected throughout the water column at 5 stations in the eastern Mediterranean Sea corresponding to the regions of the northern Aegean, mid-Aegean, western Cretan, Ionian and southern Aegean Seas. Prokaryotic abundance below 100 m declined with depth at all the stations, while decreasing trends with depth in prokaryotic heterotrophic activity were present only at 2 out of the 5 stations. Bacterial community composition (BCC), determined using both automated rRNA intergenic spacer analysis and terminal-restriction-fragment length polymorphism, was also related to depth although the number of operational taxonomic units was remarkably constant throughout the water column. Overall, the maximums in similarity values of the BCC between water sample pairs decreased with increasing temperature–salinity (T–S) distance of the water samples probably due to distinct biogeochemical characteristics of water masses. However, considerable dissimilarity in the BCC between samples with identical T–S values, and hence within the same water mass, was also observed, possibly reflecting heterogeneity in the organic matter field or in biotic control within a given water body. Thus, we conclude that the richness of bacterial communities is remarkably constant with depth down to bathypelagic waters. The similarity of bacterial communities in water parcels with identical temperature and salinity can range from highly similar to very dissimilar, reflecting variability in substrate supply despite the physical uniformity of water parcels. KEY WORDS: Bacteria · Community composition · Patchiness · Spatial scale · Eastern Mediterranean Sea Full text in pdf format PreviousNextCite this article as: Yokokawa T, De Corte D, Sintes E, Herndl GJ (2010) Spatial patterns of bacterial abundance, activity and community composition in relation to water masses in the eastern Mediterranean Sea. Aquat Microb Ecol 59:185-195. https://doi.org/10.3354/ame01393 Export citation RSS - Facebook - Tweet - linkedIn Cited by Published in AME Vol. 59, No. 2. Online publication date: April 08, 2010 Print ISSN: 0948-3055; Online ISSN: 1616-1564 Copyright © 2010 Inter-Research.

BackgroundSharks are in severe global decline due to human exploitation. The additional concern of emerging diseases for this ancient group of fish, however, remains poorly understood. While wild-caught and captive sharks may be susceptible to bacterial and transmissible diseases, recent reports suggest that shark skin may harbor properties that prevent infection, such as a specialized ultrastructure or innate immune properties, possibly related to associated microbial assemblages. To assess whether bacterial community composition differs between visibly healthy and insulted (injured) shark skin, we compared bacterial assemblages of skin covering the gills and the back from 44 wild-caught black-tip reef sharks (Carcharhinus melanopterus) from the Amirante Islands (Seychelles) via 16S rRNA gene amplicon sequencing.ResultsShark skin-associated bacterial communities were diverse (5971 bacterial taxa from 375 families) and dominated by three families of the phylum Proteobacteria typical of marine organisms and environments (Rhodobacteraceae, Alteromonadaceae, Halomonadaceae). Significant differences in bacterial community composition of skin were observed for sharks collected from different sites, but not between healthy or injured skin samples or skin type (gills vs. back). The core microbiome (defined as bacterial taxa present in ≥50% of all samples) consisted of 12 bacterial taxa, which are commonly observed in marine organisms, some of which may be associated with animal host health.ConclusionThe conserved bacterial community composition of healthy and injured shark skin samples suggests absence of severe bacterial infections or substantial pathogen propagation upon skin insult. While a mild bacterial infection may have gone undetected, the overall conserved bacterial community implies that bacterial function(s) may be maintained in injured skin. At present, the contribution of bacteria, besides intrinsic animal host factors, to counter skin infection and support rapid wound healing in sharks are unknown. This represents clear knowledge gaps that should be addressed in future work, e.g. by screening for antimicrobial properties of skin-associated bacterial isolates.

Effect of biocrusts on bacterial community composition at different soil depths in Mediterranean semi-arid ecosystems

Multiple factors influence bacterial community diversity and composition in soils with rare earth element and heavy metal co-contamination

Gut Bacterial and Lactobacilli Communities of Weaning Piglets in Response to Mannan Oligosaccharide and Sugar Beet Pulp In vitro Fermentation

Community patterns of soil bacteria and nematodes in relation to geographic distance

This study examined the similarity of epilimnetic bacterial community composition (BCC) across several within- and among-lake spatial scales, and the environmental factors giving rise to similar bacterial communities in different lakes were also explored. Samples were collected from 13 northern and southern Wisconsin lakes representing gradients in lake size, productivity, dissolved organic carbon and humic acid contents, and pH. Hypotheses regarding patchy distribution of bacterial communities in lakes were tested by comparing samples collected from nearby (tens of meters) and distant (hundreds of meters) sampling sites in the same lake. BCC was characterized by using a molecular fingerprinting technique, automated ribosomal intergenic spacer analysis (ARISA). Overall, samples collected at the 10-m, 100-m, and between-lake scales differed by 13, 17, and 75%, respectively. Variation at these last two scales was significant. The development of within-lake variation in BCC appeared to depend on the isolation of water by lake shoreline features such as bays or narrow constrictions. ARISA profiles from northern lakes had fewer peaks and were less similar to each other than were those of the southern lakes, suggesting that regional features do not necessarily lead to the development of similar bacterial communities. Lakes at similar positions on productivity and dissolved organic carbon concentration gradients had similar bacterial communities, and bacterial diversity was positively correlated with lake productivity and water temperature. Factorial studies taking into account these gradients, as well as regional spatial scales, should provide much insight into the nature of aquatic bacterial biogeography.

In order to better understand the factors that influence bacterial diversity and community composition in moss-associated bacteria, a study of bacterial communities in four moss species collected in three seasons was carried out via high-throughput sequencing of 16S rDNA and 16S rRNA. Moss species included Cratoneuron filicinum, Pylaisiella polyantha, Campyliadelphus polygamum, and Grimmia pilifera, with samples collected in May, July, and October 2015 from rocks at Beijing Songshan National Nature Reserve. In total, the bacterial richness and diversity were high regardless of moss species, sampling season, or data source (DNA vs. RNA). Bacterial sequences were assigned to a total of 558 OTUs and 279 genera in 16 phyla. Proteobacteria and Actinobacteria were the two most abundant phyla, and Cellvibrio, Lapillicoccus, Jatrophihabitans, Friedmanniella, Oligoflexus, and Bosea the most common genera in the samples. A clustering algorithm and principal coordinate analysis revealed that C. filicinum and C. polygamum had similar bacterial communities, as did P. polyantha and G. pilifera. Metabolically active bacteria showed the same pattern in addition to seasonal variation: bacterial communities were most similar in summer and autumn, looking at each moss species separately. In contrast, DNA profiles lacked obvious seasonal dynamics. A partial least squares discriminant analysis identified three groups of samples that correlated with differences in moss species resources. Although bacterial community composition did vary with the sampling season and data source, these were not the most important factors influencing bacterial communities. Previous reports exhibited that mosses have been widely used in biomonitoring of air pollution by enriching some substances or elements in the moss-tag technique and the abundant moss associated bacteria might also be important components involved in the related biological processes. Thus, this survey not only enhanced our understanding of the factors which influence microbial communities in mosses but also would be helpful for better use and development of the moss-tag technique in the environmental biomonitoring.

Increased similarity of aquatic bacterial communities of different origin after antibiotic disturbance

Both biogeographical and rainfall manipulation studies show that soil water content can be a strong driver of microbial community composition. However, we do not yet know if these patterns emerge because certain bacterial taxa are better able to survive at dry soil moisture regimes or if they are due to other drought-sensitive ecosystem properties indirectly affecting microbial community composition. In this study, we evaluated (1) whether bacterial community composition changed under an 11-year drought manipulation and (2) whether shifts under drought could be explained by variation in the moisture sensitivity of growth among bacterial taxa (moisture niche partitioning). Using 454 pyrosequencing of 16S rRNA, we observed shifts in bacterial community composition under drought, coincident with changes in other soil properties. We wet-up dry soils from drought plots to five moisture levels, and measured respiration and the composition of actively growing communities using bromodeoxyuridine (BrdU) labeling of DNA. The field drought experiment affected the composition of the active community when incubated at different moisture levels in the laboratory, as well as short-term (36-hour) respiration rates. Independent of history, bacterial communities also displayed strong niche partitioning across the wet-up moisture gradient. Although this indicates that moisture has the potential to drive bacterial community composition under long-term drought, species distributions predicted by response to moisture did not reflect the community composition of plots that were subjected to long-term drought. Bacterial community structure was likely more strongly driven by other environmental factors that changed under long-term drought, or not shaped by response to water level upon wet-up. The approach that we present here for linking niches to community composition could be adapted for other environmental variables to aid in predicting microbial species distributions and community responses to environmental change.

Modern agricultural practices have undeniably increased global food production. On the other hand, agricultural practices not only lead to a degradation of natural ecosystems but also affect the functioning of ecosystems and the related services they provide. Even though impacts of anthropogenic activities vary across ecosystems, freshwater ecosystems are among those affected to a higher degree. In comparison to surface water ecosystems, groundwater ecosystems are less affected by anthropogenic pollutants, as the overlaying soil retains organic and inorganic substances. However, it has become evident that the excessive use of fertilizers has led to the eutrophication of many aquifers. Bacterial communities, which significantly contribute to the cycling of matter due to their metabolic capacities, are prone to environmental perturbations, and structural variation of bacterial communities may consequently affect the functioning of groundwater ecosystems. Our present paper intends to evaluate the impact of anthropogenic activities on environmental conditions as well as on the structural properties of bacterial communities in groundwater. We repeatedly sampled emerging groundwater at five spring sites belonging to different catchments and determined the concentration of abiotic variables as well as the diversity and composition of bacterial communities on a local scale. We hypothesized that anthropogenic activities influence the concentration of abiotic variables, especially of nitrate, as well as the composition and diversity of bacterial communities in groundwater. Our results show that underground spring catchment areas only slightly differ regarding the concentration of abiotic variables as well as the structure of bacterial communities. Furthermore, abiotic variables, presumably influenced by anthropogenic activities, do not correlate with the diversity and composition of bacterial communities. Although supported only by circumstantial evidence, we suggest that upwelling groundwater from the deeper aquifer affects the diversity and composition of bacterial communities, and we argue that bacterial communities act as useful indicators for environmental changes.

Bacterial diversity and community composition changes in paddy soils that have different parent materials and fertility levels

SummaryTo quantify the major environmental drivers of stream bacterial population dynamics, we modelled temporal differences in stream bacterial communities to quantify community shifts, including those relating to cyclical seasonal variation and more sporadic bloom events. We applied Illumina MiSeq 16S rRNA bacterial gene sequencing of 892 stream biofilm samples, collected monthly for 36‐months from six streams. The streams were located a maximum of 118 km apart and drained three different catchment types (forest, urban and rural land uses). We identified repeatable seasonal patterns among bacterial taxa, allowing their separation into three ecological groupings, those following linear, bloom/trough and repeated, seasonal trends. Various physicochemical parameters (light, water and air temperature, pH, dissolved oxygen, nutrients) were linked to temporal community changes. Our models indicate that bloom events and seasonal episodes modify biofilm bacterial populations, suggesting that distinct microbial taxa thrive during these events including non‐cyanobacterial community members. These models could aid in determining how temporal environmental changes affect community assembly and guide the selection of appropriate statistical models to capture future community responses to environmental change.

pH dynamics and bacterial community composition in the rumen of lactating dairy cows