Mapping the niche space of soil microorganisms using taxonomy and traits

The biodiversity of microbial communities has important implications for the stability and functioning of ecosystem processes. Yet, very little is known about the environmental factors that define the microbial niche and how this influences the composition and activity of microbial communities. In this study, we derived niche parameters from physiological response curves that quantified microbial respiration for a diverse collection of soil bacteria and fungi along a soil moisture gradient. On average, soil microorganisms had relatively dry optima (0.3 MPa) and were capable of respiring under low water potentials (-2.0 MPa). Within their limits of activity, microorganisms exhibited a wide range of responses, suggesting that some taxa may be able to coexist by partitioning the moisture niche axis. For example, we identified dry-adapted generalists that tolerated a broad range of water potentials, along with wet-adapted specialists with metabolism restricted to less-negative water potentials. These contrasting ecological strategies had a phylogenetic signal at a coarse taxonomic level (phylum), suggesting that the moisture niche of soil microorganisms is highly conserved. In addition, variation in microbial responses along the moisture gradient was linked to the distribution of several functional traits. In particular, strains that were capable of producing biofilms had drier moisture optima and wider niche breadths. However, biofilm production appeared to come at a cost that was reflected in a prolonged lag time prior to exponential growth, suggesting that there is a trade-off associated with traits that allow microorganisms to contend with moisture stress. Together, we have identified functional groups of microorganisms that will help predict the structure and functioning of microbial communities under contrasting soil moisture regimes.     

DNA damage induced by ultraviolet radiation in coral-reef microbial communities

Ultraviolet radiation (UVR) has been implicated in coral-bleaching processes and UVR may create stress to marine organisms by damage to DNA. Absorption of energy from UVB (280 to 320 nm) induces direct damage to DNA via cyclobutane pyrimidine dimer photoproduct-formation. We examined the extent of DNA damage created by UVR in coral reef microbial communities and whether the coral-surface microlayer (CSM) provides protection from UVR to the microorganisms found there. Diel patterns and depth profiles of UVR effects were examined in coral mucus (coral-surface microlayer, CSM) from Montastraea faveolata and Colpophyllia natans, and water-column samples of similar depths. UV-induced photodamage was determined using a radioimmunoassay specific for cyclobutane pyrimidine dimers (thymine dimers). Significant photodamage was detected in water-column and CSM samples, although the level of damage in CSM samples was consistently lower than in water-column samples collected from the same depth, suggesting the presence of photoprotective mechanisms within the CSM. Diel patterns of photodamage were detected in both water-column and CSM samples, but peak damage occurred earlier in the day for the CSM samples, suggesting differences in damage and repair kinetics between the water column and CSM. The results suggest that microorganisms within the CSM are afforded some protection from UVR stress and that changes in the amount of DNA damage in these organisms may be an indicator of changing UVR stress to corals. Received: 10 January 1997 / Accepted: 15 September 1997     

油藏微生物群落分布及提高采收率的模拟实验研究

对取自大庆油田各类油藏的126个地层油水样品中部分微生物进行了培养计数和分析,检测出大庆油田地层水中含有好氧和厌氧微生物9类.在此基础上,进行了微生物提高石油采收率的物理模拟试验.结果表明,通过激活油藏地层水中的微生物,可以使油藏压力上升0.2MPa,并提高采收率幅度9%以上.     

Antimicrobial activities of marine sponges from the Mediterranean Sea

Extracts from marine sponges collected along the French coast of Mediterranean in 1983 have been tested for antibacterial and antifungal activities. The distribution of antimicrobial activities against five classes of microorganisms (5 Gram-positive and 5 Gram-negative terrestrial bacteria, 10 marine bacteria, 15 human pathogenic fungi and 5 phytopathogenic fungi) among 28 species of marine demosponges is reported. Antibacterial activity against Gram-positive bacteria (77%) is much more frequent than against Gram-negative bacteria (53%). Activity against marine bacteria and yeast is less frequent (32%). Those sponges which contain a large quantily of symbiotic bacteria display a weak antifungal activity.     

Combined use of eDNA metabarcoding and video surveillance for the assessment of fish biodiversity

Monitoring communities of fish is important for the management and sustainability of fisheries and marine ecosystems. Baited remote underwater video systems (BRUVs) are among the most effective nondestructive techniques for sampling bony fishes and elasmobranchs (sharks, rays, and skates). However, BRUVs sample visually conspicuous biota; hence, some taxa are undersampled or not recorded at all. We compared the diversity of fishes characterized using BRUVs with diversity detected via environmental DNA (eDNA) metabarcoding. We sampled seawater and captured BRUVs imagery at 48 locales that included reef and seagrass beds inside and outside a marine reserve (Jurien Bay in Western Australia). Eighty-two fish genera from 13 orders were detected, and the community of fishes described using eDNA and BRUVs combined yielded >30% more generic richness than when either method was used alone. Rather than detecting a homogenous genetic signature, the eDNA assemblages mirrored the BRUVs’ spatial explicitness; differentiation of taxa between seagrass and reef was clear despite the relatively small geographical scale of the study site (∼35 km²). Taxa that were not sampled by one approach, due to limitations and biases intrinsic to the method, were often detected with the other. Therefore, using BRUVs and eDNA in concert provides a more holistic view of vertebrate marine communities across habitats. Both methods are noninvasive, which enhances their potential for widespread implementation in the surveillance of marine ecosystems.     

Relevant variables to predict macrophyte communities in running waters

In both predictive theoretical and empirical models for aquatic plant communities in running waters, the development and competition are many times explained in terms of nutrients. Minerals necessary for growth are generally not assumed to be limiting, although they influence the important pH-value. At the same time it is known that factors such as oxygen-concentration, solar energy, salinity, dimension of the system and soil characteristics (including river sediments) influence the development of the community, and should be considered in modelling. Effects of water quantity and water quality on macrophytes are reviewed. These conditions are caused by processes in the landscape, characterised by a set of nested variables which explain the distribution of macrophyte species and communities. Relevant variables are described and grouped on three scales: regional, local and site conditions. Case studies with direct and indirect gradient analysis are presented. Statistical tests (stepwise regression with forward selection) reveal that each species distribution is explained by a characteristic set of relevant variables, ranging from soil type and dimension of the system, to nutrient and salinity concentration.     

Using vertebrate environmental DNA from seawater in biomonitoring of marine habitats

Conservation and management of marine biodiversity depends on biomonitoring of marine habitats, but current approaches are resource-intensive and require different approaches for different organisms. Environmental DNA (eDNA) extracted from water samples is an efficient and versatile approach to detecting aquatic animals. In the ocean, eDNA composition reflects local fauna at fine spatial scales, but little is known about the effectiveness of eDNA-based monitoring of marine communities at larger scales. We investigated the potential of eDNA to characterize and distinguish marine communities at large spatial scales by comparing vertebrate species composition among marine habitats in Qatar, the Arabian Gulf (also known as the Persian Gulf), based on eDNA metabarcoding of seawater samples. We conducted species accumulation analyses to estimate how much of the vertebrate diversity we detected. We obtained eDNA sequences from a diverse assemblage of marine vertebrates, spanning 191 taxa in 73 families. These included rare and endangered species and covered 36% of the bony fish genera previously recorded in the Gulf. Sites of similar habitat type were also similar in eDNA composition. The species accumulation analyses showed that the number of sample replicates was insufficient for some sampling sites but suggested that a few hundred eDNA samples could potentially capture >90% of the marine vertebrate diversity in the study area. Our results confirm that seawater samples contain habitat-characteristic molecular signatures and that eDNA monitoring can efficiently cover vertebrate diversity at scales relevant to national and regional conservation and management.     

Antimicrobial activities of extracts from Indo-Pacific marine plants against marine pathogens and saprophytes

This study is the second of two surveys designed to systematically screen extracts from marine plants for antimicrobial effects against ecologically relevant marine microorganisms, and to compare results on a geographical basis. In the preceding survey, extracts from tropical Atlantic marine algae and seagrasses were screened in growth inhibition assays against the pathogenic fungus Lindra thalassiae, the saprophytic fungus Dendryphiella salina, the saprophytic stramenopiles, Halophytophthora spinosa and Schizochytrium aggregatum, and the pathogenic bacterium Pseudoaltermonas bacteriolytica. In this study, the same assay microorganisms were used to examine the antimicrobial effects of lipophilic and hydrophilic extracts from 54 species of marine algae and two species of seagrasses collected from Indo-Pacific reef habitats. Overall, 95% of all species surveyed in this study yielded extracts that were active against one or more, and 77% yielded extracts that were active against two or more assay microorganisms. Broad-spectrum activity against three or four assay microbes was observed in the extracts from 50 to 21% of all species, respectively. Extracts from the green alga Bryopsis pennata and the red alga Portieria hornemannii inhibited the growth of all assay microorganisms. Given that antimicrobial activity was prevalent among extracts of Indo-Pacific marine plants, it is interesting to note that the inhibitory effects of each extract varied considerably between the assay microorganisms. Overall, H. spinosa and D. salina were the most susceptible while L. thalassiae, S. aggregatum, and P. bacteriolytica were the most resistant to the extracts tested. These results provide good evidence that antimicrobial chemical defenses are widespread among Indo-Pacific marine plants. Further, the activity profiles of plant extracts suggest that antimicrobial secondary metabolites can have pathogen-selective or broad-spectrum effects. To confirm these results, chemical studies will be needed to isolate and characterize the compounds responsible for the observed antimicrobial activities.     

Integrated biomonitoring assessment of the Lesina Lagoon (Southern Adriatic Coast, Italy): preliminary results

An integrated biomonitoring program for marine and coastal ecosystems quality assessment combines the chemical characterization of a site with the evaluation of the possible structure alterations of its living communities. This can be considered an useful tool for better identifying the summarized effects of all the components interacting with the biota. Such an integrated procedure was carried out for the assessment of the quality of the Lesina Lagoon (Southern Adriatic Coast, Italy). The water parameters levels showed a high primary production (2-6 μg l^-1); the sediment and pore water toxicity bioassays recorded a low or moderate diffused toxicity. Besides, the benthic meiofauna community structure was characterized by prevalent Nematoda taxa with a homogeneous spatial distribution. On these basis, the Lesina Lagoon seems to be characterized by a prevalent organic pollution mainly related to agricultural and zootechnical activities which, due to the lagoon's conformation, presents a homogeneous spatial distribution.     

我国硝基苯的海水水质基准及生态风险评估研究

以一种重要的化工原料硝基苯为研究对象,通过收集、筛选我国本土物种的硝基苯海水生物毒性数据,同时针对我国海区生物特点补充8种典型海洋受试生物的毒理学实验,应用物种敏感度分布(SSD)方法推导了用于保护水生生物的我国硝基苯海水水质基准值。在此基础上,尝试应用2种概率生态风险评估方法初步评估了硝基苯在我国东海椒江口水体中的生态风险。研究结果表明,用于保护我国海水生物的硝基苯水质基准高值为1.42 mg·L-1,低值为0.037 mg·L-1,与应用SSD方法推导的硝基苯淡水水质基准差异不大。商值概率分布法和联合概率曲线法的风险表征结果表明,硝基苯对椒江口中的水生生物存在潜在的生态风险,需要管理部门采取一定的风险管控措施。研究结果有望为我国水质基准、生态风险研究及硝基苯的海水水质标准制定提供参考。     

Multiple determinants of community structure in shallow marsh habitats,Cape Fear River estuary,North Carolina,USA

The nekton of tidal creeks was studied at 17 sampling localities from September 1977 through August 1978, in the Cape Fear River estuary, North Carolina, USA. Prior to these dates, collections were made at 9 stations beginning in January 1977; these data were used to supplement conclusions drawn from the larger effort. Species recruited from the ocean utilized marsh habitats only temporarily and dominated the catches with over 70% of the total abundance. Their distribution was influenced by salinity gradients and to a lesser extent by substrate characteristics. In addition, temporal habitat partitioning with associated size differences of related species played an important role in structuring marsh nekton communities. A clearly defined ecotone was associated with the mesohaline-polyhaline transition zone, in slainities between 14 and 21 S. Numerous marine stenohaline forms were restricted to salinities above 16 S, thus increasing species richness in high salinity marshes. Despite differences in freshwater flows in 1977 and 1978, major features of the various marsh communities (species associations and relative abundances) exhibited little change throughout the Cape Fear estuary, indicating that these communities were relatively persistent in time. Standing crops for ocean-spawned species at the end of the growing season indicated that considerable annual export in the form of living biomass of fish and shellfish takes place from the marshes. Since most individuals of these species return to the ocean in the fall, an important energy link between the marshes and nearshore marine environment is demonstrated.     

肠道微生物受环境污染的影响及其对宿主疾病的调控作用

宿主肠道内存在的大量微生物与其健康状况直接相关,这些微生物是人和动物健康成长不可或缺的。肠道微生物通过多种途径调节人体生理功能的同时也受到人体内外环境的影响。因此,分析建立肠道微生物、相关疾病的产生原因和作用机制以及环境影响因子之间的联系具有重要意义。本文首先针对肠道微生物对人体的物质与能量代谢、先天和获得性免疫、胃肠道功能等方面的影响进行综述。然后重点分析了近年来有关肠道微生物对环境污染所致健康效应的影响及作用机制的研究进展。以期加深肠道微生物与人类健康之间相互作用机理的理解,并为环境毒理学与肠道微生物之间关系的研究提供新的思路。     

Use of Ordination Techniques to Follow Community Succession from Oil Impact to Recovery in the Field

Much effort has been directed toward elucidating pollution effects on marine benthic communities (Pearson and Rosenberg, 1978; Sanders et al., 1980; NAS 1985). Less effort has been directed at methods of data analysis which will identify distribution patterns and relationships between communities. Traditional community structure summary parameters such as species richness and various indices of diversity utilize only part of the information contained in a data set and are not very useful in elucidating relationships between communities of animals.     

海洋微生物来源的天然产物开发研究进展

综述了近年来海洋微生物来源天然产物研究的新进展,总结了该类天然产物的开发策略.通过对样品采用不同的预处理方式、不同的分离培养基以及新的培养方法,讨论如何获得海洋来源的特有微生物和增加海洋来源微生物类群的多样性.阐述了在海洋微生物天然产物的开发过程中,采用宏基因组技术及基因组测序等手段,来发现难培养或不可培养微生物中的天然产物以及处于"沉默"状态的天然产物.最后介绍了异源生物合成、组合生物合成以及核糖体工程等技术在海洋微生物天然产物开发和改造中的应用,并举例论述了海洋微生物天然产物的开发.     

海洋环境基因组学在海洋生态研究中的应用

海洋环境基因组学是功能基因组学的一个分支学科,它将基因组学的最新技术引入到海洋生态环境的研究当中,得到了许多有价值的研究成果,显示出巨大的发展潜力。文章总结了海洋环境基因组学所开展的工作和已取得的成果,指出目前海洋环境基因组学的工作主要集中在三个领域:海洋生物基因资源文库的建立与完善;海洋生物对环境胁迫的应激反应及生理机制的研究;探索不同生物种群的基因表达谱是否与生物地理分布相关联。并着重讨论了利用基因组学技术研究环境胁迫对海洋生物物种的分布、生物物种间的相互作用以及水生物疾病的影响。如海洋环境基因组学通过测定基因表达谱的变化,研究海洋生物对环境温度的生理响应,绘制出生物地理图谱;通过测定基因转录水平的变化,更深入地了解温度变化所造成的生理支出,从而预测热气候漂移可能给海洋生态环境所造成的影响。在水生物疾病的研究方面,海洋环境基因组学用DNA微阵列技术分析染病生物的基因表达谱,筛选出发生变化的基因表达,为理解病毒感染机制提供了大量信息。还可以深入研究环境胁迫因子与微生物种群群落的组成关系,并由此找到通过维持水体的微生态平衡来消除某些病害发生的环境条件。     

Benthic macrophyte communities in the Ghar El Melh lagoon (North Tunisia)

This work deals with the biodiversity and distribution of benthic macrophytes in the Ghar El Melh lagoon, a Mediterranean coastal lagoon located in the North of Tunisia. An inventory was made of the benthic flora and submerged macrophyte communities were mapped during two successive campaigns (the summer of 1999 and the winter of 2000). The following 24 macrophyte species were identified: seven red algae, two brown algae, 11 green algae, and four marine angiosperms. The results were compared with available data from the literature. Ruppia cirrhosa is the most dominant species. It is found in all lagoon parts, except in the west sector.Ruppia beds are usually associated withCladophora forming heterogeneous communities. During summerRuppia cirrhosa shows a large distribution, covering an area of ca. 21.4 km², with dense, extensive beds covering 80–100%. In winter, severalCladophora species have a very large distribution as well, covering nearly an area of 28.5 km² with an average cover of 46%. The green algaeCaulerpa prolifera is confined to the eastern part of the lagoon which is mainly affected by seawater. In comparison with previous situations, many transformations were observed in biodiversity and spatial distribution of the dominant communities. Thus,Cymodocea nodosa andZostera beds, which dominated in the 1970s, were replaced byZostera andCaulerpa prolifera in the 1980s and are currently succeeded byRuppia cirrhosa andCladophora. Restoration of the Ghar El Melh lagoon will enable an increase in the exchange with the open sea and the circulation of water, in particular in the confined zones. This should considerably improve the water quality and would positively influence the phytobenthic communities.     

Biogeography of bacterioplankton in lakes and streams of an Arctic tundra catchment

Bacterioplankton community composition was compared across 10 lakes and 14 streams within the catchment of Toolik Lake, a tundra lake in Arctic Alaska, during seven surveys conducted over three years using denaturing gradient gel electrophoresis (DGGE) of PCR-amplified rDNA. Bacterioplankton communities in streams draining tundra were very different than those in streams draining lakes. Communities in streams draining lakes were similar to communities in lakes. In a connected series of lakes and streams, the stream communities changed with distance from the upstream lake and with changes in water chemistry, suggesting inoculation and dilution with bacteria from soil waters or hyporheic zones. In the same system, lakes shared similar bacterioplankton communities (78% similar) that shifted gradually down the catchment. In contrast, unconnected lakes contained somewhat different communities (67% similar). We found evidence that dispersal influences bacterioplankton communities via advection and dilution (mass effects) in streams, and via inoculation and subsequent growth in lakes. The spatial pattern of bacterioplankton community composition was strongly influenced by interactions among soil water, stream, and lake environments. Our results reveal large differences in lake-specific and stream-specific bacterial community composition over restricted spatial scales (<10 km) and suggest that geographic distance and connectivity influence the distribution of bacterioplankton communities across a landscape.     

Potential of Marine Reserves to Cause Community-Wide Changes beyond Their Boundaries

Abstract:  Fishing and other human activities can alter the abundances, size structure, and behavior of species playing key roles in shaping marine communities (e.g., keystone predators), which may in turn cause ecosystem shifts. Despite extensive evidence that cascading trophic interactions can underlie community-wide recovery inside no-take marine reserves by protecting high-level predators, the spatial extent of these effects into adjacent fished areas is unknown. I examined the potential for community-wide changes (i.e., the transition from overgrazed coralline barrens to macroalgal beds) in temperate rocky reefs within and around a no-take marine reserve. For this purpose I assessed distribution patterns of predatory fishes, sea urchins, and barrens across the reserve boundaries. Predatory fishes were significantly more abundant within the reserve than in adjacent locations, with moderate spillover across the reserve edges. In contrast, community-wide changes of benthic assemblages were apparent well beyond the reserve boundaries, which is consistent with temporary movements of predatory fishes (e.g., foraging migration) from the reserve to surrounding areas. My results suggest that no-take marine reserves can promote community-wide changes beyond their boundaries.     

Hagfish in the New Zealand fjords are supported by chemoautotrophy of forest carbon

Forest litter is often considered to be a minor energy source to marine communities due to its refractory nature. Large volumes of forest litter are deposited in the New Zealand fjords, and likely recycled into available energy by microbial activity. In this study we used evidence from stable isotope analyses to test whether recycled carbon from chemoautotrophs was an important contributor to the diet of hagfish (Eptatretus cirrhatus). We then analyzed fatty acid biomarkers from the chemoautotrophic clam Solemya parkinsoni and E. cirrhatus to further discriminate the contribution of marine, terrestrial, and chemoautotrophic sources. Bulk isotopic signatures of E. cirrhatus varied considerably (delta13C, from -29.2 per thousand to -16.7 per thousand; delta15N, from -2.8 per thousand to +15.5 per thousand; delta34S, from -21.7 per thousand to +16.7 per thousand) and indicated that a significant percentage of organic matter (38-51%) originated from chemoautotrophs (delta13C, -31.3 per thousand +/- 0.1 per thousand [mean +/- SE]; delta15N, -5.7 per thousand +/- 0.2 per thousand; delta34S, -32.per thousand +/- 3.8 per thousand). Fatty acid biomarkers were depleted in 13C, particularly cis-vaccenic acid (18:1omega7: delta13C, -39.0 per thousand) indicating specific microbial origins of carbon. A high proportion of forest litter in sediments, coupled with isotopic and fatty acid biomarker results, indicates that terrestrial organic matter is a dominant contributor to this marine benthic system. This study demonstrates a clear linkage between terrestrial and marine ecological processes.