Diagnostic microbial microarrays in soil ecology

Soil microbial communities are responsible for important physiological and metabolic processes. In the last decade soil microorganisms have been frequently analysed by cultivation-independent techniques because only a minority of the natural microbial communities are accessible by cultivation. Cultivation-independent community analyses have revolutionized our understanding of soil microbial diversity and population dynamics. Nevertheless, many methods are still laborious and time-consuming, and high-throughput methods have to be applied in order to understand population shifts at a finer level and to be better able to link microbial diversity with ecosystems functioning. Microbial diagnostic microarrays (MDMs) represent a powerful tool for the parallel, high-throughput identification of many microorganisms. Three categories of MDMs have been defined based on the nature of the probe and target molecules used: phylogenetic oligonucleotide microarrays with short oligonucleotides against a phylogenetic marker gene; functional gene arrays containing probes targeting genes encoding specific functions; and community genome arrays employing whole genomes as probes. In this review, important methodological developments relevant to the application of the different types of diagnostic microarrays in soil ecology will be addressed and new approaches, needs and future directions will be identified, which might lead to a better insight into the functional activities of soil microbial communities.     

Linking soil process and microbial ecology in freshwater wetland ecosystems

Soil microorganisms mediate many processes such as nitrification, denitrification, and methanogenesis that regulate ecosystem functioning and also feed back to influence atmospheric chemistry. These processes are of particular interest in freshwater wetland ecosystems where nutrient cycling is highly responsive to fluctuating hydrology and nutrients and soil gas releases may be sensitive to climate warming. In this review we briefly summarize research from process and taxonomic approaches to the study of wetland biogeochemistry and microbial ecology, and highlight areas where further research is needed to increase our mechanistic understanding of wetland system functioning. Research in wetland biogeochemistry has most often been focused on processes (e.g., methanogenesis), and less often on microbial communities or on populations of specific microorganisms of interest. Research on process has focused on controls over, and rates of, denitrification, methanogenesis, and methanotrophy. There has been some work on sulfate and iron transformations and wetland enzyme activities. Work to date indicates an important process level role for hydrology and soil nutrient status. The impact of plant species composition on processes is potentially critical, but is as yet poorly understood. Research on microbial communities in wetland soils has primarily focused on bacteria responsible for methanogenesis, denitrification, and sulfate reduction. There has been less work on taxonomic groups such as those responsible for nitrogen fixation, or aerobic processes such as nitrification. Work on general community composition and on wetland mycorrhizal fungi is particularly sparse. The general goal of microbial research has been to understand how microbial groups respond to the environment. There has been relatively little work done on the interactions among environmental controls over process rates, environmental constraints on microbial activities and community composition, and changes in processes at the ecosystem level. Finding ways to link process-based and biochemical or gene-based assays is becoming increasingly important as we seek a mechanistic understanding of the response of wetland ecosystems to current and future anthropogenic perturbations. We discuss the potential of new approaches, and highlight areas for further research.     

Biofilms and biodiversity: an interactive exploration of aquatic microbial biotechnology and ecology

The study of biofilms provides a unique educational opportunity to examine ecosystems, biodiversity and applications of environmental biotechnology. There are many variables that could be studied for measuring the interactions between bacterial biofilms and invertebrate biodiversity as a method for assessing the health of aquatic ecosystems. These interactions also lend themselves to an easily replicated model system which can be used to reach a wide audience with an educational opportunity for students as well as a professional development opportunity for teachers. At the foundation of the research are invaluable basic microbiology skills: strain collection, isolation, cultivation and characterization. Through the additional process of characterizing, identifying and enumerating invertebrate organisms that attach to bacterial biofilms in aquatic ecosystems, there evolved a multidisciplinary class laboratory activity that has found broad application. This activity is captivating not only to undergraduate microbiology students but to middle and high school students and their teachers. The demand for information about the activity has led to the development of a truly interactive web-based lesson, which in turn has resulted in additional inquiries and further refinement of the lesson as an undergraduate independent research course. Both of these are freely accessible on the web, with growing international participation and data exchange. Journal of Industrial Microbiology & Biotechnology (2000) 24, 334–338. Received 19 April 1999/ Accepted in revised form 17 February 2000     

Advances in monitoring soil microbial community dynamic and function

Microorganisms are vital to the overall ecosystem functioning, stability, and sustainability. Soil fertility and health depend on chemical composition and also on the qualitative and quantitative...     

Microbial ecology and biodiversity in permafrost

Permafrost represents 26% of terrestrial soil ecosystems; yet its biology, essentially microbiology, remains relatively unexplored. The permafrost environment is considered extreme because indigenous microorganisms must survive prolonged exposure to subzero temperatures and background radiation for geological time scales in a habitat with low water activity and extremely low rates of nutrient and metabolite transfer. Yet considerable numbers and biodiversity of bacteria exist in permafrost, some of which may be among the most ancient viable life on Earth. This review describes the permafrost environment as a microbial habitat and reviews recent studies examining microbial biodiversity found in permafrost as well as microbial growth and activity at ambient in situ subzero temperatures. These investigations suggest that functional microbial ecosystems exist within the permafrost environment and may have important implications on global biogeochemical processes as well as the search for past or extant life in permafrost presumably present on Mars and other bodies in our solar system.     

The microbial loop concept as used in terrestrial soil ecology studies

Components and processes in the aquatic microbial loop are compared with the composition and functioning of the soil microbial loop. Relative to their bacterial and/or fungal food sources, many of the soil water-film fauna (e.g., protozoa, nematodes) are conspicuous by low biomasses and high turnover rates of carbon and mineral nutrients. Comparisons with production and turnover rates of aerial (pore-inhabiting) fauna are made, and the highly patchy nature of soil microhabitats is shown to be similar to that of aquatic (marine) habitats.     

Evolutionary ecology and the conservation of biodiversity

Studies on evolving interactions among species and the coevolutionary process have suggested that the conservation of biodiversity requires a broad geographic perspective, if the `interaction biodiversity' of the earth is to be conserved with its species diversity. Continued maintenance of the geographic mosaic of specialization, defense and population structure appears to be crucial to the coevolutionary process and the long-term persistence of some interspecific interactions.     

Quantitative comparisons ofin situ microbial biodiversity by signature biomarker analysis

Microscopic examinations have convinced microbial ecologists that the culturable microbes recovered from environmental samples represent a tiny proportion of the extant microbiota. Methods for recovery and enzymatic amplification of nucleic acids from environmental samples have shown that a huge diversity existsin situ, far exceeding any expectations which were based on direct microscopy. It is now theoretically possible to extract, amplify and sequence all the nucleic acids from a community and thereby gain a comprehensive measure of the diversity as well as some insights into the phylogeny of the various elements within this community. Unfortunately, this analysis becomes economically prohibitive if applied to the multitude of niches in a single biome let alone to a diverse set of environments. It is also difficult to utilize PCR amplification on nucleic acids from some biomes because of coextracting enzymatic inhibitors. Signature biomarker analysis which potentially combines gene probe and lipid analysis on the same sample, can serve as a complement to massive environmental genome analysis in providing quantitative comparisons between microniches in the biome under study. This analysis can also give indications of the magnitude of differences in biodiversity in the blome as well as provide insight into the phenotypic activities of each community in a rapid and cost-effective manner. Applications of signature lipid biomarker analysis to define quantitatively the microbial viable biomass of portions of an Eastern USA deciduous forest, are presented.     

分子生态学研究与运行多样性保护

分子生态学的发展揭开了生物多样性保护研究的新篇章,分子技术的应用克服了传统生态学法中的一些难题,如野外调查周期长,分辨率有限,实验条件不易控制等,应用各种分子标记（如：RFLP,VNTR,RAPD,DNA测序等）可以分析种群地理格局和异质种群动态,确定种群间的基因流,研究瓶颈效应对种群的影响以及确定个体间的亲缘关系等等,所有这些研究都是指导物种保护和淑危种群的恢复所必要的,种或品系特异性的分子标记技术能够解决形态分类中的模糊现象,确定基于遗传物质的谱系关系,还可以用来分析近缘种间杂交问题,这些问题的解决有助于确定物种优先保护顺序,选择保护地工,近年来引起重视的主要组织人性复合体（MHC）NDA异分析可能会在研究种群对疾病的易感性第一系列种群特异性问题方面非常有用,随着分子技术的不断发展,会有更多的保护生物学问题得到解决,尤其是结合野外调查统计数据应用多个分子标记对目标种群进行研究,所得到的结果会更精确,更有说服力。     

土壤微生物多样性及其环境影响因子研究进展

土壤中存在丰富的微生物资源,不同土壤系统具有不同的微生物群落,微生物多样性既依赖于生态系统又服务于生态系统。本文从物种多样性、遗传多样性、生态类型多样性、功能多样性四个方面对土壤微生物多样性进行了新的诠释,总结论述了土壤微生物多样性与环境因子如土壤、植物群落和气候条件之间的关系,并对目前存在的问题和今后面临的挑战提出几点看法。     

Multivariate analyses in microbial ecology

Environmental microbiology is undergoing a dramatic revolution due to the increasing accumulation of biological information and contextual environmental parameters. This will not only enable a better identification of diversity patterns, but will also shed more light on the associated environmental conditions, spatial locations, and seasonal fluctuations, which could explain such patterns. Complex ecological questions may now be addressed using multivariate statistical analyses, which represent a vast potential of techniques that are still underexploited. Here, well-established exploratory and hypothesis-driven approaches are reviewed, so as to foster their addition to the microbial ecologist toolbox. Because such tools aim at reducing data set complexity, at identifying major patterns and putative causal factors, they will certainly find many applications in microbial ecology.     

Landscape ecology and urban biodiversity in tropical Indonesian cities

Indonesia has recently been faced with a number of great problems: poverty, natural disasters such as tsunami, earthquakes, flooding and typhoons, volcanic eruptions, loss of biodiversity, decreasing water quality and quantity, increased pollution, and aesthetic degradation of the landscape. These disturbances have been caused by rapid changes in land use and land cover, deforestation, the application of monoculture farming systems in commercial agriculture, urbanization, industrialization, and other types of infrastructure development. The government, urban communities and companies have promoted some programs to ameliorate the problem of environmental degradation. The government has ratified law no. 26/2007 as a commitment to sustainability; this law ensures that cities are obliged to provide green open spaces covering a minimum of 30% of urbanized areas. Many metropolitan cities have feverishly enacted policies to promote greening programs, such as those applied in Jakarta. However, a new town—Sentul City—has engaged in policies that aim to create a well-designed eco-city with urban greenery and ecological networks. This new policy is supposed to herald a better future for urban quality. It is expected that green spaces will provide environmental services: water resource management, biodiversity conservation, carbon sequestration, and landscape beauty.     

Community genomics in microbial ecology and evolution

It is possible to reconstruct near-complete, and possibly complete, genomes of the dominant members of microbial communities from DNA that is extracted directly from the environment. Genome sequences from environmental samples capture the aggregate characteristics of the strain population from which they were derived. Comparison of the sequence data within and among natural populations can reveal the evolutionary processes that lead to genome diversification and speciation. Community genomic datasets can also enable subsequent gene expression and proteomic studies to determine how resources are invested and functions are distributed among community members. Ultimately, genomics can reveal how individual species and strains contribute to the net activity of the community.     

Fish and mucus-dwelling bacteria interact to produce a kairomone that induces diel vertical migration in Daphnia

1. Bacterial populations associated with fish have previously been documented to be crucial for the production of chemical signals governing the interactions between predator fish and zooplankton prey. 2. In this study, we investigated the roles of fish and mucus‐dwelling bacteria in kairomone production by conducting two sets of experiments related to elimination of bacteria with antibiotics and using fish mucus in bioassays of Daphnia pulex’s diel vertical migration. 3. Daphnia’s migratory response to the antibiotic‐treated fish was about half the strength of the response to the fish cue treatment. Furthermore, when the same antibiotic‐treated fish were removed from the antibiotic‐containing water and transferred into control water for 24 and 48 h, the extent of D. pulex’s migration depended on the length of the incubation period, apparently corresponding to the regeneration of bacterial colonies associated with mucus. The migration pattern observed in the 24 h treatment was similar to that of antibiotic‐treated fish. On the other hand, a pronounced migration occurred in the 48 h following antibiotic treatment; here, we found a higher density of fish surface dwelling bacteria than at the start of the experiment. 4. In the experiment involving fish mucus, the mucus‐enriched control water induced a weak response similar to antibiotic‐treated fish. 5. On the basis of the results from the two experiments, we suggest that both fish and fish mucus‐dwelling bacteria interact in the release of kairomone in ecologically relevant quantities.