Microbial community dynamics in the forefield of glaciers

Retreating ice fronts (as a result of a warming climate) expose large expanses of deglaciated forefield, which become colonized by microbes and plants. There has been increasing interest in characterizing the biogeochemical development of these ecosystems using a chronosequence approach. Prior to the establishment of plants, microbes use autochthonously produced and allochthonously delivered nutrients for growth. The microbial community composition is largely made up of heterotrophic microbes (both bacteria and fungi), autotrophic microbes and nitrogen-fixing diazotrophs. Microbial activity is thought to be responsible for the initial build-up of labile nutrient pools, facilitating the growth of higher order plant life in developed soils. However, it is unclear to what extent these ecosystems rely on external sources of nutrients such as ancient carbon pools and periodic nitrogen deposition. Furthermore, the seasonal variation of chronosequence dynamics and the effect of winter are largely unexplored. Modelling this ecosystem will provide a quantitative evaluation of the key processes and could guide the focus of future research. Year-round datasets combined with novel metagenomic techniques will help answer some of the pressing questions in this relatively new but rapidly expanding field, which is of growing interest in the context of future large-scale ice retreat.     

干旱区高寒湿地逆行演替下土壤微生物群落结构的研究

【目的】探究高寒湿地逆行演替对土壤性质与微生物群落结构的影响。【方法】以新疆巴音布鲁克天鹅湖高寒湿地为研究对象,依托逆行演替典型样带(沼泽-沼泽化草甸-草甸),利用高通量测序技术分析各演替区土壤微生物群落结构。【结果】高寒湿地逆行演替改变了土壤微生物在分类操作单元(operational taxonomic unit,OTU)水平上的物种组成,致使草甸区的微生物ACE、Chao1、Simpson、Shannon多样性指数显著低于沼泽区和沼泽化草甸区(P<0.05);随着演替发生,变形菌门(Proteobacteria)、酸杆菌门(Acidobacteria)、拟杆菌门(Bacteroidetes)、子囊菌门(Ascomycota)的相对丰度均减少,放线菌门(Actinobacteria)、芽单胞菌门(Gemmatimonadetes)、担子菌门(Basidiomycota)、被孢霉门(Mortierellomycota)的相对丰度增加;主坐标法分析(principal coordinates analysis,PCoA)排序分析显示,土壤微生物群落在各逆行演替都出现不同程度的离散...     

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.     

The West Indies as a laboratory of biogeography and evolution

Islands have long provided material and inspiration for the study of evolution and ecology. The West Indies are complex historically and geographically, providing a rich backdrop for the analysis of colonization, diversification and extinction of species. They are sufficiently isolated to sustain endemic forms and close enough to sources of colonists to develop a dynamic interaction with surrounding continental regions. The Greater Antilles comprise old fragments of continental crust, some very large; the Lesser Antilles are a more recent volcanic island arc, and the low-lying Bahama Islands are scattered on a shallow oceanic platform. Dating of island lineages using molecular methods indicates over-water dispersal of most inhabitants of the West Indies, although direct connections with what is now southern Mexico in the Early Tertiary, and subsequent land bridges or stepping stone islands linking to Central and South America might also have facilitated colonization. Species-area relationships within the West Indies suggest a strong role for endemic radiations and extinction in shaping patterns of diversity. Diversification is promoted by opportunities for allopatric divergence between islands, or within the large islands of the Greater Antilles, with a classic example provided by the Anolis lizards. The timing of colonization events using molecular clocks permits analysis of colonization-extinction dynamics by means of species accumulation curves. These indicate low rates of colonization and extinction for reptiles and amphibians in the Greater Antilles, with estimated average persistence times of lineages in the West Indies exceeding 30Myr. Even though individual island populations of birds might persist an average of 2Myr on larger islands in the Lesser Antilles, recolonization from within the archipelago appears to maintain avian lineages within the island chain indefinitely. Birds of the Lesser Antilles also provide evidence of a mass extinction event within the past million years, emphasizing the time-heterogeneity of historical processes. Geographical dynamics are matched by ecological changes in the distribution of species within islands over time resulting from adaptive radiation and shifts in habitat, often following repeatable patterns. Although extinction is relatively infrequent under natural conditions, changes in island environments as a result of human activities have exterminated many populations and others--especially old, endemic species--remain vulnerable. Conservation efforts are strengthened by recognition of aesthetic, cultural and scientific values of the unique flora and fauna of the West Indies.     

河南宝天曼不同林龄与林型森林土壤的细菌群落结构与多样性

采用高通量16S rRNA标签测序法,比较了地处北亚热带与暖温带过渡带的宝天曼自然保护区不同林龄与林分类型的土壤细菌群落结构及多样性.结果表明： 宝天曼森林土壤细菌以变形菌门(29%)、酸杆菌门(18.5%)、疣微菌门(10%)等为主,共检测到60门1209属,优势属主要有疣微菌门的DA101(6.3%)、酸杆菌门的Acidobacteria 2(5.9%)和Candidatus Solibacter(2.9%)、泉古菌门的Candidatus Nitrososphaera(2.6%)等.不同林龄和林分类型土壤分别具有特有的种属组成及高丰度和低丰度种属.林龄与林分类型都对土壤微生物群落结构影响显著,且林分类型的影响大于林龄.80年林龄的锐齿栎土壤菌群多样性在不同林龄和林分类型中均最低.pH、土壤全氮、有机碳等是不同林龄及林分类型下土壤菌群结构变化的重要影响因子.     

覆盖模式对旱作农田土壤微生物多样性及群落结构的影响

土壤微生物是表征土壤质量的敏感指标,采用Illumina HiSep技术分析不同覆盖方式对半湿润易旱区农田土壤微生物群落结构及多样性的影响,以期从微生物的角度评价农田不同覆盖措施对土壤质量的影响。设3种覆盖模式：平作塑料薄膜覆盖（P）、平作秸秆覆盖（S）和垄膜沟播覆盖（R）,以平作不覆盖为对照（CK）,研究不同覆盖模式下土壤微生物群落变化,分析各土壤理化因子与微生物群落之间的关系。研究结果表明各覆盖处理显著改变了土壤微生物的群落结构和多样性。所有土壤样品中,细菌群落的优势菌门是变形菌门（Proteobacteria）、酸杆菌门（Acidobacteria）、放线菌门（Actinobacteria）,丰度分别为29.69%、28.28%和20.76%,CK处理下较高的土壤pH和低NO₃-N含量抑制了土壤中酸杆菌门（Acidobacteria）的生长繁殖,而放线菌门（Actinobacteria）相对丰度为所有处理中最高。真菌群落的优势菌门是子囊菌门（Ascomycota）、担子菌门（Basidiomycota）,丰度分别为59.65%和20.96%,S处理下过低的土壤温度抑制了担子菌门（Basidiomycota）生长和繁殖,其相对丰度为所有处理中最低。与CK相比,P和R处理显著提高土壤细菌的多样性和丰富度;S和R处理下土壤真菌多样性和丰富度显著增加,而P处理的土壤真菌多样性和丰富度均无显著差异。斯皮尔曼相关分析表明土壤细菌多样性主要受土壤含水量（SM）和硝态氮含量（NO₃-N）影响,而土壤真菌多样性主要受土壤温度（ST）、全氮（TN）和硝态氮含量（NO₃-N）影响;RDA分析表明微生物群落结构的变化主要受SM、ST、NO₃-N和TN含量的影响。总的来说,R处理下土壤细菌和真菌的多样性和丰富度较CK处理显著提高,该处理下土壤中担子菌门（Basidiomycota）和球囊菌（Glomeromycota）相对丰度为所有处理中最高,两者分别形成的外生菌根和从生菌根不但促进了根部养分的吸收,而且提高了作物的抗逆性,且结果证明该处理的作物产量为最高,因此在半湿润旱作区推荐采用垄膜沟播覆盖种植方式。     

Genetic isolation by distance in Arabidopsis thaliana: biogeography and postglacial colonization of Europe

Arabidopsis thaliana provides a useful model system for functional, evolutionary and ecological studies in plant biology. We have analysed natural genetic variation in A. thaliana in order to infer its biogeographical and historical distribution across Eurasia. We analysed 79 amplified fragment length polymorphism (AFLP) markers in 142 accessions from the species' native range, and found highly significant genetic isolation by distance among A. thaliana accessions from Eurasia and southern Europe. These spatial patterns of genetic variation suggest that A. thaliana colonized central and northern Europe from Asia and from Mediterranean Pleistocene refugia, a trend which has been identified in other species. Statistically significant levels of multilocus linkage disequilibrium suggest intermediate levels of disequilibrium among subsets of loci, and analysis of genetic relationships among accessions reveal a star or bush-like dendrogram with low bootstrap support. Taken together, it appears that there has been sufficient historical recombination in the A. thaliana genome such that accessions do not conform to a tree-like, bifurcating pattern of evolution - there is no 'ecotype phylogeny.' Nonetheless, significant isolation by distance provides a framework upon which studies of natural variation in A. thaliana may be designed and interpreted.     

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.     

甲烷及三氯乙烯驯化对垃圾填埋场覆盖土细菌群落结构的影响

对典型垃圾填埋覆盖土进行CH₄原位富集和三氯乙烯(TCE)驯化,研究了其生物氧化能力和微生物群落结构变化.覆盖土CH₄氧化速率为0.20～0.87 μmol·g^-1 soil·h^-1,TCE降解速率为0.009～0.013 mg·L^-1·h^-1,其中山东垃圾填埋场覆盖土土样甲烷氧化活性高于广东、上海和重庆地区土样.通过Illumina MiSeq测序技术分析了α多样性和驯化前后微生物菌群结构变化规律.结果表明: 在所有被注释的操作分类单元聚类结果中,细菌OTUs分配为39个门,85个纲,562个属,富集驯化后变形杆菌门、拟杆菌门、绿弯菌门和酸杆菌门仍为各土样的优势菌群,所占比例之和高于77.4%;γ-变形杆菌纲、β--变形杆菌纲、α-变形杆菌纲、放线菌纲和酸杆菌纲所占比例之和高于26.5%.嗜甲基菌属、厌氧绳菌属、节杆菌属和假单胞菌属经TCE驯化后,其相对丰度呈增加趋势.表明在覆盖土氯代烃生物降解过程中,除了被广泛认可的甲烷氧化菌异养共代谢机制以外,还存在非甲烷共代谢机制和氯代烃自养降解机制.     

Bacterial community structure in a latitudinal gradient of lakes: the roles of spatial versus environmental factors

1. We analysed the latitudinal variation of bacterioplankton in 45 freshwater environments (lakes, shallow lakes and ponds) across a transect of more than 2100 km stretching from Argentinean Patagonia (45°S) to Maritime Antarctica (63°S), to determine the factors that mainly determine bacterioplankton community structure. 2. Bacterioplankton community composition (BCC) was assessed by a fingerprinting method (denaturing gradient gel electrophoresis) followed by band sequencing, whereas the abundances of total bacteria and picocyanobacteria were estimated by epifluorescence microscopy. 3. Bacterioplankton community composition was controlled by a combination of spatial (latitude and longitude) and environmental [e.g. phosphate, light diffuse attenuation coefficient (K_d) and dissolved organic carbon] factors. Total bacterioplankton abundance declined with latitude. A multiple regression analysis showed that phosphate, K_d and latitude had significant effects on total bacterioplankton abundance. 4. Of 76 operational taxonomic units identified in the studied lakes, 45 were shared between Patagonian and Antarctic water bodies, 28 were present only in Patagonian lakes and three were restricted to the Antarctic lakes. Significant differences were found in BCC between Patagonia and Antarctica. Among the sequences, 54% were similar (>97% sequence similarity) to others reported from cold habitats elsewhere on the planet (glaciers, high mountain lakes, Arctic). 5. Our results provide new evidence that supports the hypotheses of biogeographic patterns of bacterial assemblages and suggest that both spatial and environmental factors control bacterioplankton community structure.     

Phylogeny and biogeography of the parrot genus Prioniturus (Aves: Psittaciformes)

The parrot genus Prioniturus occurs in the oceanic Philippines, Palawan and Wallacea, a geologically dynamic region with a complex history of land and sea. The described taxa of Prioniturus have been variously placed in different assemblages, and different numbers of species have been recognized. However, a phylogenetic framework is so far lacking. This would be the prerequisite to reconstructing dispersal and colonization patterns of Prioniturus across and within Wallacea and the Philippines. Following our robustly supported phylogenetic hypothesis based on two mitochondrial genes, we propose to treat Prioniturus mindorensis comb. nov. as well as Prioniturus montanus and Prioniturus waterstradti as separate species. In Prioniturus discurus discurus and Prioniturus discurus whiteheadi, further studies using additional data and specimens are necessary to clarify their taxonomic status. This result is congruent with other studies demonstrating that alpha diversity of the Philippine avifauna is strongly underestimated. According to our biogeographic reconstruction, Prioniturus has diversified by a complex combination of colonization of islands and subsequent divergence in allopatry among and within island groups. Dispersal between Sulawesi/Wallacea and the Philippines occurred twice and documents a rare case of faunal exchange between these two regions.     

施肥梯度对高寒草甸群落结构、功能和土壤质量的影响

在三江源区研究了不同施肥梯度对高寒矮嵩草草甸群落结构、功能;土壤全量养分、速效养分;土壤有机碳和微生物生物量碳的影响,以揭示矮嵩草草甸群落特征;土壤养分和土壤微生物活性对施肥梯度的响应.结果表明:1)随着施肥量的增加,不同功能群的盖度响应各异,其中禾本科植物的响应较大,而豆科和杂类草植物盖度明显降低,莎草科盖度变化不明显;施肥量增加到一定程度,如施氮40 g/m2时,各功能群植物的盖度逐渐降低.生物量随施肥梯度呈单峰曲线变化,不施肥时生物量最低,施肥20 g/m2或32 g/m2时生物量最高.2)土壤全量养分和速效养分在施肥量为20 g/m2或32 g/m2时较高,施肥量增加到40 g/m2时土壤资源逐渐降低.3)不同施肥梯度矮嵩草草甸土壤有机碳和微生物生物量碳在0-10 cm土层明显较高,且随着施肥量的增加,分布在0-40 cm土层的土壤有机碳含量呈单峰曲线变化.施肥20 g/m2或32 g/m2时土壤有机碳和微生物量碳含量最高.4)30 g/m2施肥量可作为高寒草甸最佳施氮水平.施肥梯度下土壤有机碳和微生物量碳含量可作为衡量土壤肥力和土壤质量变化的重要指标.高施肥量(≥40 g/m2)视为影响高寒草甸生态系统结构与功能、土壤养分及土壤微生物活性的阈值.     

健康与感染青枯病烟株根际土壤与茎秆细菌群落结构与多样性

【目的】了解健康烟株与感染青枯病烟株在根际土壤、茎杆发病部位、茎杆病健交界部位以及未发病茎杆的细菌群落结构与多样性。【方法】分别对土壤与茎杆样品中细菌的16S rRNA基因V3-V4区进行扩增,采用Illumina MiSeq测序技术对扩增片段进行高通量测序,然后对健康烟株与感染青枯病烟株不同部位细菌群落结构与多样性进行分析。【结果】感染青枯病烟株发病茎杆及根际土壤的细菌群落多样性高于健康烟株茎杆及其根际土壤样品,病健交界茎杆样品细菌群落多样性低于健康烟株。变形菌门(Proteobacteria)在所有样品中均为优势菌门;所有烟株根际土壤的优势菌门为拟杆菌门(Bacteroidetes)、酸杆菌门(Acidobacteria)、放线菌门(Actinobacteria)和绿弯菌门(Chloroflexi);健康烟株茎杆部位的优势菌门为蓝细菌门(Cyanobacteria);感染青枯病烟株发病茎杆和病健交界茎杆部位的优势菌门为蓝细菌门(Cyanobacteria)和厚壁菌门(Firmicutes)。所有根际土壤样品的优势菌属为劳尔氏菌属(Ralstonia)、假单胞菌属(Pseudomonas)、鞘脂单胞菌属(Sphingomonas)、黄杆菌属(Flavobacterium)和代尔夫特菌属(Delftia),而感染青枯病烟株根际土壤的劳尔氏菌属(Ralstonia)和假单胞菌属(Pseudomonas)相对丰度显著高于健康烟株根际土壤,鞘脂单胞菌属相对丰度显著低于健康烟株根际土壤。烟株茎杆的优势菌属为劳尔氏菌属和假单胞菌属等。感染青枯病烟株病健交界茎杆中劳尔氏菌属、肠杆菌属(Enterobacter)和泛菌属(Pantoea)相对丰度显著低于健康烟株样品。【结论】健康与感染青枯病烟株茎杆样品细菌群落的丰富度和多样性明显低于相应的根际土壤样品。较健康烟株而言,感染青枯病烟株根际土壤和茎杆样品细菌群落丰富度和多样性均表现出不同程度地增加,且根际土壤细菌群落结构变化较茎杆样品明显,而病健交界茎杆样品细菌群落丰富度和多样性降低。烟草青枯病为典型土传病害,其病原茄科劳尔氏菌尽管能在烟株维管束中蔓延扩增,但主要还是分布于土壤中;它的存在似乎对土壤细菌群落的影响大于茎杆样品的。该研究结果提示对于青枯病的防治不能局限于烟株本身,田间土壤也应加大防治力度。     

祁连山东缘高寒草甸灌丛化对植被群落与土壤理化特性的影响

为明晰祁连山东缘高寒草甸灌丛化对其植被群落与土壤理化特性的影响,选取甘肃省天祝藏族自治县高寒草甸灌丛化区域,调查其植被,采集土壤测定理化性质,分析植被与土壤的互馈关系。结果表明:高寒草甸植被的均匀度指数、高度、盖度、地上生物量、土壤含水率随灌丛化过程增加(P<0.05),而多样性指数和容重均降低;全磷含量在各土层以灌丛区最高,但C ∶ P和N ∶ P以草甸区最高;土壤N ∶ P<14表明土壤养分主要受限于氮;土壤脲酶和过氧化氢酶活性在草甸区各土层显著高于灌丛区(P<0.05);冗余分析显示前两个排序轴的累计解释量为54.88%,土壤过氧化氢酶与植被特征拟合的结果最好(Pr=0.010),表明高寒草甸灌丛化过程中土壤过氧化氢酶受植被特征的制约最大。可见,高寒草甸灌丛化显著影响了植被群落结构与土壤理化特性,在祁连山生态保护和管理中应该予以重视。     

高山森林土壤微生物群落结构和功能对模拟增温的响应

将高山森林土壤装入PVC管中(土壤有机层在上、矿质土壤层在下)培养10周,以高山森林土壤年均温为对照,采用室内人工气候箱分别模拟增温2和4 ℃,研究土壤微生物群落和土壤酶活性对温度升高的响应.结果表明: 温度升高显著降低了土壤有机层中细菌、矿质土壤层中革兰氏阴性菌(G^-)PLFAs含量,但对土壤真菌无显著影响.温度升高引起革兰氏阳性菌和阴性菌比值(G⁺/G^-)升高,改变了微生物群落结构.增温对漆酶、β-葡萄糖酶、酸性磷酸酶和N-乙酰葡糖胺糖苷酶活性没有显著影响.土壤微生物群落之间呈现出协同增长的趋势,真菌、细菌、G⁺、G^-等微生物群落之间均呈显著正相关.土壤有机层中β-葡萄糖苷酶与土壤微生物群落对碳源利用的竞争,导致β-葡萄糖苷酶活性与土壤有机层细菌、真菌、G⁺呈显著负相关.高山森林不同土壤微生物类群对增温的响应不同,细菌比真菌对温度的响应更敏感,真菌对增温有一定的耐受能力.     

黑龙江省表层冻土细菌群落结构组成和功能特征

冻土是气候变化的敏感区,冻土中细菌对于预测冻土和气候之间的潜在反馈机制至关重要,研究冻土区土壤中细菌的多样性和种群结构将有助于及时检测环境变化并采取有效的应对措施。以黑龙江省表层冻土为研究对象,运用Illumina MiSeq高通量测序分析技术,系统分析黑龙江表层冻土细菌群落结构组成和功能特征,探究影响因素。结果表明,得到的785640条原始序列可划分为30个门,109个纲,209个目,326个科,512个属,598个种。优势菌门主要包括Proteobacteria、Actinobacteria、Acidobacteria、Chloroflexi、Bacteroidetes、Verrucomicrobia,在P<0.01水平上,Proteobacteria与Actinobacteria、Chloroflexi极显著负相关,与Acidobacteria极显著正相关,Actinobacteria与Acidobacteria极显著负相关,与Chloroflexi极显著正相关,Acidobacteria和Chloroflexi之间则无显著相关性。属水平上,Aetherobacter属在各...     

Comparative phylogeography of two coastal polychaete tubeworms in the Northeast Atlantic supports shared history and vicariant events

The historic processes which have led to the present-day patterns of genetic structure in the marine coastal fauna of the Northeast Atlantic are still poorly understood. While tectonic uplifts and changes in sea level may have caused large-scale vicariance, warmer conditions during glacial maxima may have allowed pockets of diversity to persist to a much wider extent than in the Northwestern Atlantic. The large-scale geographic distribution of deeply divergent lineages of the coastal polychaete tubeworms Pectinaria koreni (two clades) and Owenia fusiformis (three clades) were compared using a fragment of the mitochondrial cytochrome oxidase I gene (mtCOI). All lineages were present along the biogeographic transition zone on the north coast of Brittany (France) and we found evidence pointing towards congruence in the timing of cladogenic events between Pectinaria sp. (P. auricoma/P. belgica and P. koreni) and Owenia sp., suggesting a shared history of vicariant events. More conserved 16SrRNA sequences obtained from four species of Pectinariidae together with mtCOI sequences of P. koreni seem consistent with an initial establishment of pectinariids in the north, and a southward colonization of the Northeast Atlantic. Phylogeographic patterns in O. fusiformis were also consistent with a north/south pattern of lineage splitting and congruent levels of divergence were detected between lineages of both species. We observed signatures of both persistence in small northern glacial refugia, and of northwards range expansion from regions situated closer to the Mediterranean. However, whether the recolonization of the Northeast Atlantic by both species actually reflects separate interglacial periods is unclear with regards to the lack of molecular clock calibration in coastal polychaete species.