现代分子生物学技术在冰川微生物生态研究中的应用

研究冰川中微生物的多样性对于揭示环境气候变迁,研究生物进化,开发微生物资源具有重要意义,现代分子生物学的发展为研究冰川微生物的多样性提供了行之有效的方法.简要综述了16S rDNA文库构建、变性梯度凝胶电泳、限制性片段长度多态性和荧光原位杂交等技术的原理及在冰川微生物生态研究中的应用现状.     

冰川微生物菌群分布及多样性研究技术进展

冰川微生物蕴涵着生命进化历程的丰富信息,对冰川微生物的研究将为揭示遗传多样性、气候环境变迁及其对环境变化的响应机制等开辟新途径。阐述了冰川微生物的多样性和群落结构特征、影响其分布的生态因素,并进一步对冰川微生物研究所涉及的分子生物学方法进行了综述。     

三极冰川冰尘微生物及其介导的碳氮生物地球化学循环研究进展

冰尘是散落在冰川表面由矿物质、有机质和微生物组成的聚合体,其主要来源包括远源输送来的细粉尘和气溶胶组分、局地源的粗冰碛物及来自周围生态系统的土壤和植物碎屑等。冰尘对太阳辐射具有较强的吸收作用,可降低冰面反照率、促进冰川融化。冰尘也是迄今为止生物多样性最高的冰川表面微生物栖息地,生活着细菌、真菌、藻类等。冰尘微生物是冰川表面地球化学循环的主要驱动者,微生物分解转化冰尘内有机质,降低冰川表面反照率影响冰川物质平衡。基于冰尘的重要性,本文综述了南极、北极、青藏高原第三极冰川冰尘的物理和化学特征及其影响因素,冰尘微生物群落组成及其介导的碳氮生物地球化学循环过程,并展望了冰尘微生物研究的前景。     

冰川微生物菌群分布的研究概况及其前景

冰川中以耐冷的生物为主,形成一个以微生物为主要生命形式的相对简单的生态系统.冰川中的微生物包括病毒、细菌、放线菌、丝状真菌、酵母菌和藻类.其中一些病毒对人类健康具有潜在的危害性.着重论述了不同区域和不同海拔高度的冰川微生物类群和数量分布特征以及冰芯（深冰川）细菌菌群分布与气候环境的关系.综述结果表明：一些微生物类群广泛存在于各地的冰川上,具有全球分布特性;另一些类群只出现在个别冰川上,为一些地方性冰川微生物.随着海拔高度的增加,冰川上呈现出冰、雪冰和雪环境明显不同的生态条件;微生物类群分布也具有明显的差异性,与冰川上的生态条件和盛行的风向有关.优势类群对冰、雪冰和雪环境具有一定的指示意义.冰川微生物数量分布不仅受到冰川上的水热、光照和营养状况的影响,还与降雪的沉积作用有关.冰芯中的细菌数量与矿物微粒含量具有密切的对应关系.最后指出了冰川微生物研究在基因多样性、气候环境变化、生物地球化学循环、微生物对环境变化的响应机制和星际生命探索中的重要性及其生态学和社会经济意义.     

青藏高原微生物多样性研究

正青藏高原被誉为世界屋脊,其内部除平原外还有许多山峰、冰川、高山湖泊和高山沼泽,是生态环境最为奇特、生物资源最为丰富的自然资源宝库之一。同时,青藏高原的微生物群落结构及其多样性与其他区域存在巨大差异,因而具有极高的科学研究价值,并逐渐被人们所关注。研究发现气候变化对青藏高原高寒草地生态系统草丛-地境界面微生物会产生重要的影响[1]。冰川雪藻的研究主要在南部的Yala冰川开展,     

冰川前缘土壤微生物原生演替的生态特征——以乌鲁木齐河源1号冰川为例

为了解冰川前缘土壤微生物在原生演替过程中的生态特征及其影响因素,用空间距离代替时间序列,以乌鲁木齐河源1号冰川终碛堤为起点,沿6个不同演替时期(0,4,15,31,43a和对照)的样带采集土样,以冰川附近发育良好的土壤为对照,测定土壤酶活性、微生物氮矿化与脱氨作用以及微生物生物量。结果表明,土壤脲酶、蛋白酶、酸性磷酸酶、芳基硫酸酯酶、蔗糖酶活性、微生物氮矿化及脱氨作用随演替时间而增加,微生物生物量碳和氮变化呈波动状,趋势不明显。相关分析表明,土壤有机质与酶活、微生物生物量存在极显著正相关(P0.01)。1号冰川前缘微生物多样性指数随着演替时间持续增加,但目前仍未达稳定状态。     

细菌与古菌之间的直接电子传递

冰川占地球陆地表面的11%,储存了约10⁴ Pg有机碳。随着冰川消融有机碳被释放至下游生态系统中,刺激海洋、湖泊和径流的初级生产力进而影响其生态系统。微生物参与的固碳过程决定了冰川有机碳储量及向下游输出碳量。研究冰川固碳微生物群落构成及其生态功能,可为估算冰川碳积累量和保护下游生态系统提供数据基础。本文综述了冰川碳储量和释放量、冰川生态系统主要固碳途径、固碳微生物群落组成、固碳速率以及影响固碳速率的环境因素。最后基于研究现状展望了冰川生态系统固碳微生物的未来研究和发展方向。     

明永冰川垂直气候带中可培养低温细菌多样性分析

本研究对位于云南滇西北的明永冰川地区暖温带、中温带和寒温带三个不同垂直气候带中可培养低温细菌的多样性进行了研究。利用四种不同培养基对该地区可培养低温细菌进行了分离纯化,共得到细菌37 513株,根据菌落形态特征分为了391种,其中LB培养基分离到99种,Organic培养基分离到78种,PSG培养基分离到96种,PYGV培养基分离得到118种,可以看出寡营养培养基PYGV分离得到的细菌种类多于LB和Organnic等富营养培养基,表明PYGV针对冰川地区细菌的分离与鉴定更为合适;通过革兰氏染色和扫描电镜观察表明大部分菌株为革兰阴性杆菌;对已分离得到的优势菌进行了16S rRNA基因测序并构建系统发育树,分析得出:假单胞菌属(Pseudomonas)、耶尔森氏菌属(Yersinia)和黄杆菌属(Flavobacterium)在明永冰川不同垂直气候带上均有分布,其中假单胞菌属最多占据35%;而寡养单胞菌属(Stenotrophomonas)是寒温带上特有的菌属。本研究证明明永冰川地区垂直气候带中可培养低温细菌多样性非常丰富,也为下一步了解这一特殊地理生态环境下微生物的群落演替规律、研究冰川环境中微生物群落如何响应气候变化提供了参考。     

农业土壤微生物基因与群落多样性研究进展

介绍了群落基因组多样性、结构多样性与功能多样性相互关系的研究方法 ,重点论述了近年来农业土壤微生物群落遗传、结构与功能多样性的研究进展。同时总结了耕作措施和养分管理对农业土壤微生物群落多样性的影响 ,提出微生物序列分析、比较基因组学和微生物芯片技术与传统研究技术结合将有助于对微生物群落结构与功能和生物与环境因素对土壤微生物群落影响的深刻理解     

冰川消退带微生物群落演替及生物地球化学循环

冰川是生物圈重要组分之一。由于全球气候变化世界多地冰川加速消融,暴露原本被冰盖覆盖的区域,这些区域被称为冰川消退区域(glacier retreat area)或冰川前部区域(glacier foreland)。自暴露开始消退区随即发生初生演替,随着演替进行,物质循环逐步建立,生物量和土壤C、N总量逐步增加。生态系统C、N输入最初以矿化外来物为主,逐渐转变为以生物固C、固N为主。演替早期生态系统的发育主要受土壤C、N含量的限制,而演替后期的限制性营养物转变为P。演替区域土壤逐渐发育并促进生态位的分化,细菌、真菌、古菌,病毒及其他微生物群落的生物量和多样性不断增加直至达到该地区可承受的极值。随着生存条件的改善,不同生态策略物种的更替导致每个演替阶段微生物群落结构的差异。整体上,伴随演替进行微生物群落丰度、结构和活性呈现梯度性变化。气候变化对冰川消退带生态演替结果产生多方面的影响,而这些影响结果又综合反馈气候变化,因此目前难以准确估计气候变化对消退带生态演替的净效应。综述了近年冰川消退带微生物群落演替方面相关的研究结果,同时分别对该区域物质循环的建立、微生物群落演替和气候变化造成的影响这三个方面进行详细描述,并指出当前研究的不足。     

Lineage admixture during postglacial range expansion is responsible for the increased gene diversity of Kalopanax septemlobus in a recently colonised territory

We aimed to reveal the effects of range expansion and subsequent lineage admixture from separated glacial refugia on genetic diversity of Kalopanax septemlobus in Japan, by combining nuclear microsatellite data and ecological niche modelling. Allelic richness and gene diversity were compared at the population and regional level. We also statistically examined these indices as a function of population accessibility to the last glacial maximum (LGM) palaeodistribution reconstructed by ecological niche modelling to test a simple range expansion scenario from glacial refugia. Genetic diversity was highest in the populations of southern Japan and gradually decreased towards the north. However, an additional centre of genetic diversity, when measured as gene diversity, was found in northern Honshu Island, where distinct lineages were shown to be in contact. Positive effects of population accessibility to the LGM range were detected in both diversity indices at different spatial scales. The combined data support independent postglacial range expansions towards the north from the edge populations on the exposed coastal shelf of Pacific and Sea of Japan in northern Honshu during the LGM, which subsequently resulted in markedly low genetic diversity in the northernmost extant range, Hokkaido. The regional increase in gene diversity in northern Honshu is likely to be the result of postglacial lineage admixture. Relative difference in the spatial scales best relating population genetic diversity with the LGM distribution can be explained by a higher rate of allelic richness diversity loss during range expansions and stronger effects of lineage admixture on gene diversity.     

Is Niagara Falls a barrier to gene flow in riverine fishes? A test using genome‐wide SNP data from seven native species

Since the early Holocene, fish population genetics in the Laurentian Great Lakes have been shaped by the dual influences of habitat structure and post‐glacial dispersal. Riverscape genetics theory predicts that longitudinal habitat corridors and unidirectional downstream water‐flow drive the downstream accumulation of genetic diversity, whereas post‐glacial dispersal theory predicts that fish genetic diversity should decrease with increasing distance from glacial refugia. This study examines populations of seven native fish species codistributed above and below the 58 m high Niagara Falls – a hypothesized barrier to gene flow in aquatic species. A better understanding of Niagara Falls’ role as a barrier to gene flow and dispersal is needed to identify drivers of Great Lakes genetic diversity and guide strategies to limit exotic species invasions. We used genome‐wide SNPs and coalescent models to test whether populations are: (a) genetically distinct, consistent with the Niagara Falls barrier hypothesis; (b) more genetically diverse upstream, consistent with post‐glacial expansion theory, or downstream, consistent with the riverscape habitat theory; and (c) have migrated either upstream or downstream past Niagara Falls. We found that genetic diversity is consistently greater below Niagara Falls and the falls are an effective barrier to migration, but two species have probably dispersed upstream past the falls after glacial retreat yet before opening of the Welland Canal. Models restricting migration to after opening of the Welland Canal were generally rejected. These results help explain how river habitat features affect aquatic species’ genetic diversity and highlight the need to better understand post‐glacial dispersal pathways.     

Genetic diversity, but not hatching success, is jointly affected by postglacial colonization and isolation in the threatened frog, Rana latastei

Both postglacial colonization and habitat fragmentation can reduce the genetic diversity of populations, which in turn can affect fitness. However, since these processes occur at different spatial and temporal scales, the consequences of either process may differ. To disentangle the relative role of isolation and postglacial colonization in determining genetic diversity and fitness, we studied microsatellite diversity of 295 individuals from 10 populations and measured the hatch rate of 218 clutches from eight populations of a threatened frog, R. latastei. The populations that were affected by fragmentation to a greater extent suffered higher embryo mortality and reduced hatch rate, while no effects of distance from glacial refugium on hatch rate were detected. Altogether, distance from glacial refugium and isolation explained > 90% of variation in genetic diversity. We found that the genetic diversity was lowest in populations both isolated and far from the glacial refugium, and that distance from refugium seems to have the primary role in determining genetic diversity. The relationship between genetic diversity and hatch rate was not significant. However, the proportion of genetic diversity lost through recent isolation had a significant, negative effect on fitness. It is possible that selection at least partially purged the negative effects of the ancestral loss of genetic diversity.     

Direct and indirect effects of glaciers on aquatic biodiversity in high Andean peatlands

The rapid melting of glacier cover is one of the most obvious impacts of climate change on alpine ecosystems and biodiversity. Our understanding of the impact of a decrease in glacier runoff on aquatic biodiversity is currently based on the ‘glacier‐heterogeneity‐diversity’ paradigm, according to which there is high α‐diversity at intermediate levels of glacial influence due to the high degree of environmental heterogeneity caused by glacier water. This α‐diversity pattern generates high levels of between‐site aquatic community variation (high β diversity) and increases regional diversity (γ‐diversity). There is a rich conceptual background in favor of this paradigm, but empirical data supporting it are scarce. We investigated this paradigm by analyzing the different diversity patterns (α, β and γ‐diversity) of four aquatic groups (zooplankton, macroinvertebrates, algae and macrophytes) living in high‐elevation peatlands (>4500 m above sea level). We sampled 200 pools from 20 peatlands along a glacier gradient in the Cordillera Real of Bolivia. We performed structural equation modeling (SEM) to analyze the potential mechanisms underlying the observed diversity patterns. Intermediate levels of glacial influence (15–20% cover) resulted in high heterogeneity, but α‐diversity responded to glacial influence only for the zooplankton group (Cladocera). Our SEM analysis did not identify environmental heterogeneity as a significant variable explaining the relationship between glacier and α‐diversity. Peatland area had a strong positive effect on heterogeneity and diversity. β‐diversity was significantly associated with glacier gradient, and 12.9% of the total regional diversity (γ‐diversity) was restricted to peatlands with a high degree of glacial influence. These species might be lost in a context of glacial retreat. These findings provide new insight into the potential effects of glacial retreat on the aquatic environment and biodiversity in the peatlands of the tropical Andes.     

Postglacial recolonization in a cold climate specialist in western Europe: patterns of genetic diversity in the adder (Vipera berus) support the central–marginal hypothesis

Understanding the impact of postglacial recolonization on genetic diversity is essential in explaining current patterns of genetic variation. The central–marginal hypothesis (CMH) predicts a reduction in genetic diversity from the core of the distribution to peripheral populations, as well as reduced connectivity between peripheral populations. While the CMH has received considerable empirical support, its broad applicability is still debated and alternative hypotheses predict different spatial patterns of genetic diversity. Using microsatellite markers, we analysed the genetic diversity of the adder (Vipera berus) in western Europe to reconstruct postglacial recolonization. Approximate Bayesian Computation (ABC) analyses suggested a postglacial recolonization from two routes: a western route from the Atlantic Coast up to Belgium and a central route from the Massif Central to the Alps. This cold‐adapted species likely used two isolated glacial refugia in southern France, in permafrost‐free areas during the last glacial maximum. Adder populations further from putative glacial refugia had lower genetic diversity and reduced connectivity; therefore, our results support the predictions of the CMH. Our study also illustrates the utility of highly variable nuclear markers, such as microsatellites, and ABC to test competing recolonization hypotheses.     

Molecular evidence for glacial refugia of mountain plants in the European Alps

Many mountain ranges have been strongly glaciated during the Quaternary ice ages, and the locations of glacial refugia of mountain plants have been debated for a long time. A series of detailed molecular studies, investigating intraspecific genetic variation of mountain plants in the European Alps, now allows for a first synopsis. A comparison of the phylogeographic patterns with geological and palaeoenvironmental data demonstrates that glacial refugia were located along the southwestern, southern, eastern and northern border of the Alps. Additional glacial refugia were present in central Alpine areas, where high-elevation plants survived the last glaciation on ice-free mountain tops. The observed intraspecific phylogeographies suggest general patterns of glacial survival, which conform to well-known centres of Alpine species diversity and endemism. This implies that evolutionary or biogeographic processes induced by climatic fluctuations act on gene and species diversity in a similar way.     

Abundance and Diversity of Glacial Bacteria on the Tibetan Plateau with Environment

The relation of glacial microorganism and their living environment is concerned but less understood for both glaciologists and microbiologists. Here we present the results about glacial snow bacteria from 3 glaciers on the Tibetan Plateau. The concentrations and diversity of bacteria collected from snow pit samples of East Rongbuk, Laohugou and Hailuogou glaciers on the Tibetan Plateau were investigated by epifluorescence microscope, denaturing gradient gel electrophoresis and Shannon-Weaver index. Concentrations and community diversity of bacteria in the East Rongbuk glacier with lower concentration and smaller size of microparticle were lower than in the Laohugou with higher concentration and larger size of microparticle. Bacterial concentration in East Rongbuk Glacier was close to that in polar regions, suggesting that Mt. Everest is a bacterial background for remote regions away from direct influence of anthropogenic sources. In addition, altitude difference was another factor for higher concentrations and community diversity of bacteria in Hailuogou and Laohugou glaciers than in East Rongbuk Glacier. The highest concentrations and community diversity of bacteria in Hailuogou Glacier were attributed to its most diverse atmospheric circulations and highest temperature among the 3 glaciers. We suggest a complicated correlation between glacial bacteria and their regional living environments.     

Distinct or similar? Soft bottom polychaete diversity in Arctic and Antarctic glacial fjords

The main aim of this study was to compare the polychaete communities in two similar polar areas: an Arctic fjord, Hornsund (Svalbard) and an Antarctic fjord, Ezcurra Inlet (South Shetlands). This is the first attempt to compare Arctic and Antarctic diversity based on fully comparable datasets. Forty van Veen grab samples were collected in each fjord: twenty replicates were taken in each of two fjord areas characterized by a different level of glacial disturbance—in the inner (glacial bay) and outer (fjord mouth) region of both fjords, from depths of about 100 m in 2005 (Hornsund) and in 2007 (Ezcurra Inlet). In the glacial bays, species richness and diversity were significantly higher in Ezcurra Inlet than in Hornsund due to higher rate of glacial disturbance in the latter one. In the outer areas, species richness was similar in both fjords, although diversity values were higher in Ezcurra Inlet. Polychaete species richness in the habitats characterized by similar level of disturbance (outer areas of the fjords) was the same in both polar regions. At this small scale, where community drivers are very similar, the species richness seems to be independent from the local or regional species pool.     

Preliminary Study on Effects of Glacial Retreat on the Dominant Glacial Snow Bacteria in Laohugou Glacier No. 12

One impact of climate change is the rapid shrinking of glaciers, resulting in microorganisms deposited into glacial snow or ice being exposed to new environments such as glacier foreland. A pyrosequencing analysis based on the bacterial 16S rRNA gene showed that bacterial diversity was the highest in proglacial soil, followed by that of glacial snow in ablation zone, then by that of glacial snow in the accumulation area, finally by that of glacial snow in glacier terminus, with the combination of Chao1, ACE, Shannon and Simpson analysis. Eighteen phyla were detected from the 7 samples, but mainly composed of Proteobacteria, Actinobacteria and Bacteroidetes. Flavobacterium, Massilia, Pedobacter, Polaromonas were more abundant in glacial snow samples than in glacial soil sample. Massilia was rarely reported in other environments, implying the necessity for its conservation under scenarios of glacier and snowpack loss induced by climate change.     

Adding early-stage engineering species affects advanced-stage organization of shallow-water fouling assemblages

Population genetics has gained popularity as a method to discover glacial refugia in terrestrial species, but has only recently been applied to the marine realm. The last glacial maxima occurred 20,000 years ago, decreasing sea levels by 120 m and exposing much of the continental shelf in the northern Gulf of Mexico, with the exception of De Soto Canyon (2100 m depth). The goal of this study was to determine whether population dynamics of the giant deep-sea isopod, Bathynomus giganteus, were better explained by habitat diversity or by the past presence of a marine glacial refugium in De Soto Canyon. To accomplish this we (1) measured genetic diversity in De Soto Canyon and adjacent regions, (2) characterized gene flow and connectivity between these regions, and (3) investigated historical changes to population size. We sequenced three mitochondrial loci (12S, 16S, and COI) from 212 individuals and also performed a next-generation sequencing pilot study using double digest Restriction site-Associated DNA sequencing. We found high genetic diversity and connectivity throughout the study regions, migration between all three regions, low population differentiation, and evidence of population expansion. This study suggests that habitat heterogeneity, rather than the presence of a glacial refugium, has had an historical effect on the population dynamics of B. giganteus.