太湖梅梁湾水域蓝藻水华前与水华末期细菌群落结构的变化

通过16S rRNA克隆文库研究了太湖梅梁湾2004年3月和9月表层水样中细菌组成的变化,发现在蓝藻水华前与水华末期的菌群结构存在差异,特别是最优势的细菌发生了很大变化.3月水样中的克隆子主要与Bacteroidetes(42.7%)、β-Proteobacteria(18.4%)、α-Proteobacteria(16.5%)和Actinobacteria(16.5%)相关,9月水样中的克隆子主要与Cyanobacteria(28.8%)、β-Proteobacteria(25.0%)、Actinobacteria(17.3%)和α-Proteobacteria(15.4%)相关.此外,在水华末期(9月)的细菌组成更为多样性,有11个类群;而未发生水华时(3月)的细菌组成只有7个类群.同相关研究比较发现,α、β-Proteobacteria,Actinobacteria均为太湖中的常见菌群,其分布较为广泛;而γ-Proteobacteria和Firmicutes多出现于太湖的沉积物中,在水体中较少出现;属于Bacteroidetes这一类群的浮游细菌在湖水中很丰富.所研究水域中发现的很多细菌的16SrRNA基因与出现在许多不同的淡水生境,包括国外贫营养湖、中营养湖和富营养湖中细菌的系统关系密切,还发现大量源于长江的克隆子,很少有与海洋中细菌相似的序列(除Bacteroidetes门的成员外).图2表3参21     

隐球酵母Zwy-2-3循环利用油脂发酵废弃细胞产油

为提高资源利用效率,降低微生物油脂发酵成本,解决微生物油脂发酵中废弃酵母细胞和发酵废液处理排放的问题,研究隐球酵母(Cryptococcus podzolicus)Zwy-2-3利用栎类淀粉发酵产油情况,并探讨发酵废液和废弃酵母细胞酶解液作为氮源的循环利用.结果显示,以葡萄糖60 g/L和总氮0.18 g/L的废弃酵母细胞酶解液发酵时,循环3次其油脂产量分别达到6.79 g/L、6.66 g/L、6.72 g/L,均高于对照组;而将发酵废液回收用作废弃酵母细胞酶解的缓冲液时,其生物量、油脂产量同对照组相当;将该方法应用于栎类淀粉水解液同步糖化发酵产油脂的实验,循环3次后其生物量、油脂产量分别为13.04 g/L、7.13 g/L,比对照组提高了9.85%、10.03%,且3次循环的油脂含量较为稳定.油脂组分分析结果显示,菌株Zwy-2-3利用栎类淀粉同步糖化和废弃细胞循环酶解液发酵生产的微生物油脂不饱和脂肪酸的含量达到93%以上,与植物油组成相似.综上,酶解废弃酵母细胞可有效应用于酵母产油发酵,可为非粮淀粉生产的微生物油脂应用于生物柴油生产奠定基础.     

不同C/N值下亚硝酸盐氧化菌和异养菌混合体系的微生物多样性

采用PCR-RFLP技术研究了不同C/N比下亚硝酸盐氧化菌及异养菌混合体系的微牛物多样性,并探讨了微生物菌群结构与其功能(硝化件能)的关系.C/N=0时,混合体系主要由自养菌和寡营养菌(85.1%)组成,包括亚硝酸盐氧化菌(NOB)、拟杆菌门、α-变形菌纲、浮霉菌门和绿色非硫细菌中的一些菌株.C/N=0.44时,混合体系中的自养菌减少,异养菌(主要是γ-变形菌纲的成员)大量出现.C/N=8.82时,γ-变形菌纲的菌株尤其是反硝化菌Pseudomonas sp.占主导(93.8%),与此同时,随着C/N升高,该混合体系的硝化性能也由专一的亚硝酸盐氧化过程转变为同时硝化反硝化过程.微生物菌群结构的转变较好地解释了其硝化性能的改变.本研究揭示了微生物菌群结构与其功能的内在联系,同时表明PCR-RFLP技术与化学分析相结合是研究微生物菌群结构与功能的有力工具.图3表2参13     

秦皇岛近海养殖对潮间带微生物群落多样性的影响

潮间带微生物群落在驱动海岸带生态系统物质循环和能量流动中具有重要作用,近海养殖造成的环境问题日益凸显,但其对潮间带微生物群落结构的影响还缺乏研究。采用变性梯度凝胶电泳（DGGE）和限制性片段长度多态性（RFLP）的分子生物学技术,研究秦皇岛养殖区与旅游区潮间带沉积物中微生物多样性的差异,分析养殖区微生物的16S rRNA基因文库的组成特征。结果表明：养殖区的微生物群落结构与旅游区形成较大的差异,DGGE图谱中养殖区的特有条带主要集中于γ-变形菌纲（γ-proteobacteria）,还分布于α-变形菌纲（α-proteobacteria）,拟杆菌门（Bacteroidetes）,放线菌门（Actinobacteria）和厚壁菌门（Firmicutes）。影响潮间带微生物的群落结构的主要环境因子包括温度、盐度、pH和NO3-浓度,影响率达55.2%。对差异最大的洋河大桥南养殖区（Q1站）的微生物样品建立克隆文库分析群落结构,变形菌门（Proteobacteria）为优势菌群,占总群落的60%,其中γ-变形菌纲是主要存在的微生物纲,其余菌群包括放线菌门、拟杆菌门、蓝藻菌门（Cyanobacteria）和疣微菌门（Verrucomicrobia）的微生物。养殖区海岸带微生物群落中出现了与环境污染和赤潮密切相关的菌群,如拟杆菌门、肠杆菌属（Enterobacteriaceae）和α-变形细菌红细菌目（Roseovarius）的微生物。     

南极中山站排污口土壤中微生物群落的DGGE分析

以南极中山站排污口土壤为研究对象,提取样品中微生物宏基因组DNA,用变性梯度凝胶电泳(DGGE)对宏基因组DNA中的16S rRNA基因V3可变区进行分析,测定了31个不同条带所代表的序列.比较结果显示,排污口土壤样品与相同生境对照样品中的微生物类群组成均以CFB (Cytophaga-Flexibacteria-Bacteroides)类群和γ-变形菌纲(γ-Proteobacteria)为主,另外还有少量的α-, β-, δ-变形菌纲,和一些原核的藻类和革兰氏阳性细菌(G ). 但在排污口土壤样品中检出了传染性微生物毛球菌属(Trichococcus)和狡诈菌属(Dolosigranulum),以及丰富的小球藻(Chlorella),说明污水的排放已经对该地微生物群落造成明显的影响.     

祁连山冻土区土壤活动层与冻土层中甲烷代谢微生物群落结构特征

冻土土壤中的甲烷代谢微生物可氧化或产生甲烷,影响着甲烷所参与的碳循环过程,对于全球温室气体的释放和调节具有重要的作用.对祁连山冻土区土壤活动层与冻土层中的甲烷代谢微生物产甲烷菌(Methanogens)和甲烷氧化菌(Methanotrophs)的群落结构组成进行研究.通过对产甲烷菌的mcrA基因和甲烷氧化菌的pmoA基因进行PCR扩增,分别构建其基因克隆文库,并通过序列同源比对进行系统发育分析和多样性分析.结果显示:冻土土壤活动层中的产甲烷菌包括Rice cluster Ⅰ、Methanosarcinaceae、Methanomicrobiales、Methanosaetaceae、Methanobacteriaceae五种类型,而在土壤冻土层则包括了Rice cluster Ⅰ、Methanosarcinaceae、Methanobacteriaceae三种类型.土壤活动层的甲烷氧化菌由隶属于α-Proteobacteria(Type Ⅱ)的Methylocystis和隶属于γ-Proteobacteria(Type Ⅰ)的Methylobacter两种类型群体组成,而土壤冻土层中则只包括了Methylocystis这一种类型.由此可见,冻土土壤活动层与冻土层中的甲烷代谢微生物群落结构存在一定的差异.     

室温条件下油藏采出液微生物群落结构稳定性

获得准确的油藏微生物群落信息是开展油藏微生物工业化应用的重要前提.为了解油藏采出液脱离油藏环境后微生物群落结构的变化以及一个时间点的单次取样的代表性,利用目前最先进的高通量测序技术,对胜利油田油藏采出液室温放置5 d内的微生物群落结构以及连续5 d独立取样的同一油井水样间的微生物群落结构开展研究.结果显示,室内放置0-5 d过程中,细菌和古菌群落结构中的优势菌群没有发生明显改变,细菌的优势菌为热硫还原杆菌属(Thermodesulforhabdus)、无色杆菌属(Achromobacter)、沙雷氏菌(Serratia)以及一些未分类的细菌,古菌的优势菌为古生球菌属(Archaeoglobus)、产甲烷球菌属(Methanococcus)和甲烷鬃毛菌属(Methanosaeta).但是细菌和古菌的多样性存在逐渐降低的趋势,其中古菌多样性的变化比细菌更为明显.同时研究也证实同一口油井连续5 d独立取样的样品间,细菌和古菌群落结构中的优势菌群也没有发生较大的变化,与室内放置样品的优势菌属一致,多样性分析同样发现油藏内不同时间点古菌多样性的波动较细菌的大.本研究说明油藏采出液室温放置短期内优势菌群结构具有稳定性,一次取样的油水井样品具有阶段代表性,这可为高通量测序技术在油藏微生物群落结构解析中的应用提供重要理论支撑.     

低温纤维素降解菌的分离与鉴定

对内蒙古部分地区土壤中低温降解纤维素的微生物进行研究,以期获得一些高酶活的低温纤维素酶产生菌.采用纯培养的方法,在10℃下培养获得纯培养物.以细菌16S rDNA通用引物PCR扩增后进行序列同源性比对确定种属.以DNS法测定纤维素酶活性,并对酶活较高的菌株进行产酶条件的优化.结果共分离得到55株可低温降解纤维素的菌株,16S rDNA序列分析表明它们分别属于γ-变形菌纲(γ-Proteobacteria)、硬壁菌门(Firmicutes)、放线菌门(Actinobacteria)、拟杆菌门(Bacteroidetes)以及β-变形菌纲(β-Proteobacteria).该55株菌的纤维素酶活性均在22℃下最高.其中菌株CF11在10℃下的酶活在分离得到的55株细菌中最高.通过优化,菌株CF11产纤维素酶的最佳条件初步确定为pH值为6.5,培养时间为10 d,并且是以酵母提取物作为氮源,其纤维素酶活为58.091 IU.因此菌株CF11是一株极具开发潜力的低温纤维素酶产生菌.     

油井采出液中硝酸盐还原菌的分离培养及对硫酸盐还原的抑制

采用油井采出液培养基和加入无机盐成分的改良油井采出液培养基,对大庆油田萨北过渡带油井采出液中的细菌进行分离培养及初步鉴定,比较了两种情况下培养出的具有硝酸盐和/或亚硝酸盐还原,以及/或反硝化能力菌群结构的差异.利用采出液培养基培养出一组新的微生物菌株,并且分离的硝酸盐和/或亚硝酸盐还原菌,以及/或反硝化细菌(Nitrate/nitrite reducing bacteria,denitrifying bacteria,NRDB)比例明显高于无机盐-采出液培养基;但培养基中无机盐成分的添加,提高了可培养NRDB的群落生物多样性.仅仅向油井采出液中直接投加硝酸盐作为电子受体,对其中硝酸盐还原、亚硝酸盐还原和反硝化微生物(NRDB)的激活作用以及产抑制硫化物产生的能力有限,而同时加入分离自采出液的NRDB和硝酸盐则对硫酸盐还原菌(SRB)的生长和产硫化物活性都产生了明显的抑制.但是NRDB与硝酸盐同时投加对不同SRB的抑制效果并不相同,导致了SRB群落结构的变化.图5表2参17     

孤岛油田中一区馆3单元油藏微生物多样性分析

应用分子生态学方法,分析了孤岛油田中一区馆3单元油藏样品的微生物多样性,包括两个注入水样和4口油井产出液样,发现注入水样的微生物多样性明显高于油井产出液样,其中γ-变形菌纲(Gammaproteobacteria)和β-变形菌纲(Betaproteobacteria)占较高比例;同一单元相同的油藏条件下,不同油井产出液水样中微生物多样性存在明显的差异,油井产出液中的细菌类型较单一,以Gammaproteobacteria为主,但古菌类型相对较多,包含甲烷杆菌纲(Methanobacteria)、甲烷微菌纲(Methanomicrobia)、古丸菌纲(Archaeoglobi)、热球菌纲(Thermococci)等多个不同纲的微生物.相同的油井微生物多样性随时间不同而发生变化.对油藏微生物生态结构的分析可以为微生物采油技术提供基础资料.     

Rapid,recurring, structured survey versus bioblitz for generating biodiversity data and analysis with a multispecies abundance model

A bioblitz inexpensively and quickly generates biodiversity data, but bioblitzes are often conducted with haphazard, unreplicated sampling. Results tend to be taxonomically, geographically, or temporally biased, lack metadata, and consist of lists of observed taxa that do not enable further analyses or correction for imperfect detection. A rapid, recurring, structured survey (RRSS) uses a structured sampling design and temporal and spatial replication to survey randomly selected sites on a conservation property. We participated in a loosely structured bioblitz and a subsequent RRSS at Big Canoe Creek Nature Preserve in Springville (St. Clair County), Alabama (USA) to compare observed richness derived from the 2 survey approaches. The RRSS data structure enabled us to fit models that accounted for imperfect detection to estimate abundances, occupancy probabilities, and habitat associations. The loosely structured bioblitz data could not be used in such models. We present a new integrated multispecies abundance model that we applied to avian RRSS data. Our model extension enables estimation for the community, employs data augmentation to estimate the number of undetected species, and incorporates covariates. The RRSS generated a more comprehensive and less biased list of observed taxonomic richness than the loosely structured bioblitz (e.g., 73 vs. 45 bird species and 104 vs. 63 insect families from the RRSS vs. loosely structured bioblitz, respectively). Models fit to the RRSS data identified seasonal patterns in avian community composition and allowed for estimation of habitat–occupancy relationships for insect taxa. The RRSS protocol has potential for broad transferability as a standardized, quick, and inexpensive way to inventory biodiversity and estimate ecological parameters while providing an outreach opportunity.     

Compliance with and ecosystem function of biodiversity offsets in North American and European freshwaters

Land-use change via human development is a major driver of biodiversity loss. To reduce these impacts, billions of dollars are spent on biodiversity offsets. However, studies evaluating offset project effectiveness that examine components such as the overall compliance and function of projects remain rare. We reviewed 577 offsetting projects in freshwater ecosystems that included the metrics project size, type of aquatic system (e.g., wetland and creek), offsetting measure (e.g., enhancement, restoration, and creation), and an assessment of the projects’ compliance and functional success. Project information was obtained from scientific and government databases and gray literature. Despite considerable investment in offsetting projects, crucial problems persisted. Although compliance and function were related to each other, a high level of compliance did not guarantee a high degree of function. However, large projects relative to area had better function than small projects. Function improved when projects targeted productivity or specific ecosystem features and when multiple complementary management targets were in place. Restorative measures were more likely to achieve targets than creating entirely new ecosystems. Altogether the relationships we found highlight specific ecological processes that may help improve offsetting outcomes.     

A palaeo-hydrogeological model for arsenic contamination in southern and south-east Asia

An argument is presented in which areas of natural arsenic contamination of modern groundwaters throughout Asia have a common origin. Arsenic originally accumulated in oceanic ferro-manganoan sediments of the eastern Palaeo-Tethys. This was further concentrated through oceanic crustal extinction in what later became the south-east Chinese accreted mineralised terrain. Proto-Himalayan uplift of this area created the palaeo-drainage systems of the Ganges – Brahmaputra, Irrawaddy, Mekong, and Red Rivers, with consequent headwater erosion of arsenic-rich sediments. Their downstream deposition as immature and easily redistributed Neogene sandstones, silts, and iron-rich clays has created secondary and tertiary reservoirs of adsorbed and authigenic arsenic, from which the current arsenic-rich groundwaters have evolved. Considering river basins within the above palaeo-hydrogeological framework provides a basis for assessing the risk of arsenic in groundwater basins of south and south-eastern Asia.     

Cost‐effective conservation of an endangered frog under uncertainty

How should managers choose among conservation options when resources are scarce and there is uncertainty regarding the effectiveness of actions? Well‐developed tools exist for prioritizing areas for one‐time and binary actions (e.g., protect vs. not protect), but methods for prioritizing incremental or ongoing actions (such as habitat creation and maintenance) remain uncommon. We devised an approach that combines metapopulation viability and cost‐effectiveness analyses to select among alternative conservation actions while accounting for uncertainty. In our study, cost‐effectiveness is the ratio between the benefit of an action and its economic cost, where benefit is the change in metapopulation viability. We applied the approach to the case of the endangered growling grass frog (Litoria raniformis), which is threatened by urban development. We extended a Bayesian model to predict metapopulation viability under 9 urbanization and management scenarios and incorporated the full probability distribution of possible outcomes for each scenario into the cost‐effectiveness analysis. This allowed us to discern between cost‐effective alternatives that were robust to uncertainty and those with a relatively high risk of failure. We found a relatively high risk of extinction following urbanization if the only action was reservation of core habitat; habitat creation actions performed better than enhancement actions; and cost‐effectiveness ranking changed depending on the consideration of uncertainty. Our results suggest that creation and maintenance of wetlands dedicated to L. raniformis is the only cost‐effective action likely to result in a sufficiently low risk of extinction. To our knowledge we are the first study to use Bayesian metapopulation viability analysis to explicitly incorporate parametric and demographic uncertainty into a cost‐effective evaluation of conservation actions. The approach offers guidance to decision makers aiming to achieve cost‐effective conservation under uncertainty.     

Threats to intact tropical peatlands and opportunities for their conservation

Large, intact areas of tropical peatland are highly threatened at a global scale by the expansion of commercial agriculture and other forms of economic development. Conserving peatlands on a landscape scale, with their hydrology intact, is of international conservation importance to preserve their distinctive biodiversity and ecosystem services and maintain their resilience to future environmental change. We explored threats to and opportunities for conserving remaining intact tropical peatlands; thus, we excluded peatlands of Indonesia and Malaysia, where extensive deforestation, drainage, and conversion to plantations means conservation in this region can protect only small fragments of the original ecosystem. We focused on a case study, the Pastaza‐Marañón Foreland Basin (PMFB) in Peru, which is among the largest known intact tropical peatland landscapes in the world and is representative of peatland vulnerability. Maintenance of the hydrological conditions critical for carbon storage and ecosystem function of peatlands is, in the PMFB, primarily threatened by expansion of commercial agriculture linked to new transport infrastructure that is facilitating access to remote areas. There remain opportunities in the PMFB and elsewhere to develop alternative, more sustainable land‐use practices. Although some of the peatlands in the PMFB fall within existing legally protected areas, this protection does not include the most carbon‐dense (domed pole forest) areas. New carbon‐based conservation instruments (e.g., REDD+, Green Climate Fund), developing markets for sustainable peatland products, transferring land title to local communities, and expanding protected areas offer pathways to increased protection for intact tropical peatlands in Amazonia and elsewhere, such as those in New Guinea and Central Africa which remain, for the moment, broadly beyond the frontier of commercial development.     

Parasitic wasps orient to green leaf volatiles

Summary Undamaged plants emit low levels of green leaf volatiles (GLVs), while caterpillar-damaged and artificially damaged plants emit relatively higher levels of certain GLVs. Female braconid parasitoids,Microplitis croceipes, oriented to both damaged plants and to individual GLVs in no-choice tests in a wind tunnel, but seldom oriented to undamaged plants. Female ichneumonid parasitoids,Netelia heroica, also oriented to individual GLVs in a wind tunnel. Males of both wasp species failed to orient to the GLVs. These data show that leaf-feeding caterpillars can cause the release of GLVs, and that parasitic wasps can respond to these odors by flying upwind (chemoanemotactic response), which brings the wasps to their caterpillar hosts. This supports the hypothesis that plants communicate with members of the third trophic level,i.e., plants under herbivore attack emit chemical signals that guide natural enemies of herbivores to sites of plant damage. In this interaction, the GLVs serve as tritrophic plant-to-parasitoid synomones. That parasitoids from two different wasp families oriented to GLVs suggests that the response may be widespread among the Hymenoptera.Mention of a commercial or proprietary product does not constitute an endorsement by the U.S. Department of Agriculture     

Human Influence and Classical Biogeographic Predictors of Rare Species Occurrence

Biogeographic theory predicts that rare species occur more often in larger, less‐isolated habitat patches and suggests that patch size and connectivity are positive predictors of patch quality for conservation. However, in areas substantially modified by humans, rare species may be relegated to the most isolated patches. We used data from plant surveys of 81 meadow patches in the Georgia Basin of Canada and the United States to show that presence of threatened and endangered plants was positively predicted for patches that were isolated on small islands surrounded by ocean and for patches that were isolated by surrounding forest. Neither patch size nor connectivity were positive predictors of rare species occurrence. Thus, in our study area, human influence, presumably due to disturbance or introduction of competitive non‐native species, appears to have overwhelmed classical predictors of rare species distribution, such that greater patch isolation appeared to favor presence of rare species. We suggest conservation planners consider the potential advantages of protecting geographically isolated patches in human‐modified landscapes because such patches may represent the only habitats in which rare species are likely to persist. Influencia Humana y Predictores Biogeográficos Clásicos de la Ocurrencia de Especies Raras     

Seasonal dynamics of macro-algae in the South Lake of Tunis

The macro-algae communities observed in the south lake of Tunis are characterized by the predominance of nitrophilous algae which are in the order of biomass importance:Ulva, Cladophora andEnteromorpha. We have noted seasonal changes of alga distribution. The wind appears to be one of the most important factors influencing this distribution. The total biomass reaches a maximum in the spring. Rapid decomposition of the biomass leads to a severe ecological imbalance, resulting in crises of anoxia and fish death. A restoration project has already started. It aims at removal of contaminated muds and the introduction of a new circulation system. The main objectives of this work were to collect information on the distribution and biomass of the phytobenthic communities as a first step in the constitution of a database for further comparison.     

Patterns and biases of climate change threats in the IUCN Red List

International Union for Conservation of Nature (IUCN) Red List assessments rely on published data and expert inputs, and biases can be introduced where underlying definitions and concepts are ambiguous. Consideration of climate change threat is no exception, and recently numerous approaches to assessing the threat of climate change to species have been developed. We explored IUCN Red List assessments of amphibians and birds to determine whether species listed as threatened by climate change display distinct patterns in terms of habitat occupied and additional nonclimatic threats faced. We compared IUCN Red List data with a published data set of species’ biological and ecological traits believed to infer high vulnerability to climate change and determined whether distributions of climate change‐threatened species on the IUCN Red List concur with those of climate change‐threatened species identified with the trait‐based approach and whether species possessing these traits are more likely to have climate change listed as a threat on the IUCN Red List. Species in some ecosystems (e.g., grassland, shrubland) and subject to particular threats (e.g., invasive species) were more likely to have climate change as a listed threat. Geographical patterns of climate change‐threatened amphibians and birds on the IUCN Red List were incongruent with patterns of global species richness and patterns identified using trait‐based approaches. Certain traits were linked to increases or decreases in the likelihood of a species being threatened by climate change. Broad temperature tolerance of a species was consistently related to an increased likelihood of climate change threat, indicating counterintuitive relationships in IUCN assessments. To improve the robustness of species assessments of the vulnerability or extinction risk associated with climate change, we suggest IUCN adopt a more cohesive approach whereby specific traits highlighted by our results are considered in Red List assessments. To achieve this and to strengthen the climate change‐vulnerability assessments approach, it is necessary to identify and implement logical avenues for further research into traits that make species vulnerable to climate change (including population‐level threats).