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Table of Content
    Volume 21 Issue 4
    20 July 2013

    Microbes are widely distributed in ecosystems. This special issue summarizes the advances in research technologies of microbial diversity and reviews distributions, maintenance mechanisms and ecosystem functions of microbes. The cover pictures upward from left to right: Fistulina hepatica, Tremella aurantialba, Methanolobus psychrophilus; In the middle from left to right: Hericium flagellum, Mycetocola miduiensis, Pulveroboletus ravenelii;

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    Orginal Article
    Progress in the studies of microbial diversity
    Jizheng He, Liangdong Guo
    Biodiv Sci. 2013, 21 (4):  391-392.  doi:10.3724/SP.J.1003.2013.02159
    Abstract ( 1301 )   HTML ( 1 )   PDF (148KB) ( 3471 )   Save
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    Recent advancement in microbial environmental research using metagenomics tools
    Xin Sun, Ying Gao, Yunfeng Yang
    Biodiv Sci. 2013, 21 (4):  393-400.  doi:10.3724/SP.J.1003.2013.08050
    Abstract ( 2000 )   HTML ( 1 )   PDF (247KB) ( 6511 )   Save
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    Metagenomics is the study of microbial meta-genomes from environmental samples, which is independent on the ability to cultivate microbes in the laboratory. It provides a new way of examining the microbial world and has been widely used in microbiological research for the past decade. Sequencing-based metagenomic technology, represented by 454 and Illumina sequencing platforms, and microarray-based technology, often using GeoChip, are two of the most commonly used technologies in metagenomics. Sequencing-based technologies are capable of detecting new microbes and genes, but are limited with regard to sequence depth and quantification, and present problems of contamination when used on complex microbial communities. Microarray-based technologies are complementary to sequencing-based technologies in regard to advantages and disadvantages. They have been widely used, for example, in studies of climate change, energy, engineering, metallurgy, extreme environments and human health. However, their use in examining the extremely complex and diverse microbial world merits further technical development, with a focus on integrating both technologies and the development of appropriate bioinformatics tools.

    Progress in environmental transcriptomics based on next-generation high-throughput sequencing
    Yuanfeng Cai, Zhongjun Jia
    Biodiv Sci. 2013, 21 (4):  401-410.  doi:10.3724/SP.J.1003.2013.10031
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    Environmental transcriptomics, which focuses on microbial mRNA derived from complex environmental samples using the RNA-Seq method, allows investigation of expression and patterns of regulation of functional genes in natural microbial communities. This review outlines the basic protocol of environmental transcriptomics, from sample collection and preservation, total RNA isolation, mRNA enrichment, cDNA synthesis to high-throughput sequencing and data analysis. Main technological problems are pointed out, such as low yield of mRNA in environmental samples, contamination of mRNA by various impurities like humic substances and limited degree of rRNA removal. Recent progresses in specific methodologies to improve the quantity and quality of mRNA, especially in RNA extraction, purification and the enrichment of mRNA, are outlined. Bioinformatics methods that deal with the large volume of RNA-Seq data are addressed, such as quality control of the sequence data, sequence assembly, detection and removal of rRNA, gene annotation and functional classification, and detection of differently expressed genes. The widely application of environmental transcriptomics, including detection of new genes, study of gene expression and regulation of microorganisms in different environments, and the analysis of metabolic pathways of special organic substances, are also highlighted. Environmental transcriptomics, combined with the further development of sequencing technology and bioinformatics tools in the future, are likely to be comprehensively used in the study of environmental microbiology.

    Thoughts on the microbial diversity-stability relationship in soil ecosystems
    Jizheng He, Jing Li, Yuanming Zheng
    Biodiv Sci. 2013, 21 (4):  411-420.  doi:10.3724/SP.J.1003.2013.10033
    Abstract ( 1926 )   HTML ( 2 )   PDF (373KB) ( 3794 )   Save
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    The diversity-stability relationship has been a controversial topic in ecology since the 1950s. Natural ecosystems are significantly influenced by human activity, so it is necessary to explore the diversity-stability relationship in relation to environmental disturbance and loss of biodiversity. Studies on this have focused more on above-ground terrestrial ecosystem, and consequently below-ground ecosystem has tended to be neglected, especially with regard to soil microbial diversity and stability. However, soil microbial diversity is crucial to the maintenance of ecosystem functioning as soil microorganisms influence many ecosystem processes and drive biogeochemical cycles. One important aim of soil microbial diversity research is to clarify the responses of soil microorganisms to various environmental fluctuations, so as to predict ecosystem stability and ecological service function. In this paper, we briefly introduce the concepts and research approaches for examining soil microbial diversity and below-ground ecosystem stability. Furthermore, we probe into the soil microbial diversity-stability relationship. We propose that the soil microbial system is a dynamic self-organized system. It maintains its relative stability as a result of soil microbes genetically adapting to environmental disturbances through mutation. In this way, the soil microbial system becomes resistant and resilient to environmental change and consequently sustains the stability of soil ecosystems. Future emphasis in the study of the relationships between soil microbial diversity and stability should put in the coupling processes of the below-ground ecosystem and the above-ground ecosystem. It is essential to construct a theoretical framework for soil microbial ecology by learning from theories of macroscopic ecology. We need to develop some mechanistic models to quantitatively describe and predict the relationship between soil microbial diversity and ecosystem stability.

    Bacterial diversity and ecological function in lake water bodies
    Lijuan Ren, Dan He, Peng Xing, Yujing Wang, Qinglong Wu
    Biodiv Sci. 2013, 21 (4):  421-432.  doi:10.3724/SP.J.1003.2013.12052
    Abstract ( 2120 )   HTML ( 1 )   PDF (305KB) ( 3077 )   Save
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    The healthy development of lake ecosystems is a global issue. Bacteria are not only an integral component of food webs, but also play a key role in controlling and regulating water quality in lake ecosystems. Hence, in order to provide some suggestions for maintaining the long-term and healthy development of lake ecosystems, this review discusses and analyses concepts and assessment of bacterial diversity, the distribution of bacteria communities, mechanisms of formation, and the ecological functions of such communities in lake water bodies. In total, there are 21 freshwater bacterial phyla typically found in lake waters at present. Among them, Proteobacteria, Cyanobacteria, Bacteroidetes, Actinobacteria and Verrucomicrobia are the most important. The Beijerinck and Baas-Becking perspective and the meta- community hypothesis suggest that bacterial community diversity and species distributions in lake water bodies are caused by the combined action of stochastic and determinate processes. Research on the function of lake bacteria has mainly focused on processes that bacteria are involved in, for example water quality and elemental biogeochemical cycles. Despite efforts over the past 10 years, knowledge on lake bacterial community diversity and function is still very limited. Lake bacterial ecology is still a young science, which restricts people further understanding of microbial communities in lake bodies. Future research is required on: (1) integrating bacterial phenotype, genotype, phylogeny and ecological features to define the concept of bacterial “species”; (2) the dispersal of bacteria between different locations at a regional scale; (3) bacterial community diversity and functional characteristics at the micro scale; (4) ecological theories and hypotheses of bacterial community diversity in lake ecosystems to improve the theoretical framework of microbial ecology.

    Phylogenetic and functional diversity of nitrogen cycling microbes in coastal sediments
    Jun Gong, Yanjing Song, Xiaoli Zhang
    Biodiv Sci. 2013, 21 (4):  433-444.  doi:10.3724/SP.J.1003.2013.12027
    Abstract ( 2162 )   HTML ( 1 )   PDF (284KB) ( 3795 )   Save
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    The coastal zone contains diverse habitats which are usually characterized by strong environmental gradients (e.g. salinity, nutrients and pollutants). This makes the coastal zone an ideal experimental laboratory for describing microbial diversity and testing hypotheses on community structure, function and control. Coastal sediment is of significance in nutrient regeneration and transformation involving different assemblages of microbes in the nitrogen cycle. This review focuses on 16S rRNA gene-based phylogenetic diversity and the key enzyme encoding gene-based (e.g. nifH, amoA, narG, nirS, nirK, nosZ, nrfA, hzo and hzs) functional diversity of nitrogen fixing, ammonia oxidizing and anaerobic ammonia oxidation (Anammox) bacteria as well as bacteria and fungi involved in denitrification and dissimilatory nitrate reduction to ammonium (DNRA). Characteristics of community composition and diversity of nitrogen cycling microbes in different habitats (e.g. estuarine, intertidal flats, seagrass or seaweed beds, mangroves, salt marsh, coral reefs, and shallow seas), and their spatiotemporal patterns under benthic pollution or bioturbation are reviewed. Future directions for a better understanding diversity of nitrogen cycling microbes are suggested, such as culture methods and technologies, and single-cell sequencing, etc.

    Biodiversity of deep-sea microorganisms
    Fengping Wang, Yueheng Zhou, Xinxu Zhang, Xiang Xiao
    Biodiv Sci. 2013, 21 (4):  445-455.  doi:10.3724/SP.J.1003.2013.11094
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    The oceans, with an average depth of 3,800 meters and an average pressure about 38 MPa, cover about 70% of the surface of the Earth. Geological structures under the seawater, such as marine sediments, oceanic crust, hydrothermal vents, and the cold seeps, vary significantly with regard to physical and chemical properties. In combination, these diverse environments contain the largest microbial ecosystem in the world. In deep seawater, the major microorganism groups are Alpha-& Gammaproteobacteria, and Marine Group I. In deep-sea sediments, the abundance of microbes is related to the content of organic matter and distance from land. Methane Oxidizing Archaea (ANME) and sulfate reducing bacteria (Deltaproteobacteria) are common in deep-sea cold seep environments; while in hydrothermal vents, the richness and dynamics of chemical substances have led to highly diversified archaeal and bacterial groups. In contrast, the oceanic crust is mainly composed of basic and ultrabasic rocks rich in minerals, and as a result houses microorganisms that are mainly autotrophic, utilizing iron, manganese and sulfur. Because more than 99% of deep-sea microorganisms cannot be cultured, an understanding of their diversity, physiological features, and biogeochemical roles remains to be fully achieved. In this article, we review and summarize what is known about the distribution and diversity of deep-sea microorganisms in diverse habitats. It is emphasized that there is much to learn about these microbes.

    A review of microbial diversity in polar terrestrial environments
    Weidong Kong
    Biodiv Sci. 2013, 21 (4):  456-467.  doi:10.3724/SP.J.1003.2013.12043
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    Polar regions refer to the areas at high latitudes and altitudes, that are characterized by low temperature and limited nutrients, and are very vulnerable and sensitive to global climate change. They include the Antarctic, the Arctic and the Tibetan Plateau, which is recognized as “the third pole”. The harsh polar environments are inhabited by abundant microbes that shape and maintain ecosystems by driving biogeochemical cycles. This article herein reviews microbial diversity in these polar terrestrial environments, including soils, lakes and glaciers in the Antarctic, the Arctic and the Tibetan Plateau. In the three poles, five major groups of microbes have been detected, e.g. Acidobacteria, Actinobacteria, Bacteroidetes, Cynobacteria, and Firmicutes. These microbes are salt- and cold-tolerant. Research in polar microbial ecology in China is currently lagging behind developed countries. Priorities should be given to long-term observations on the Tibetan Plateau, which is easily approached. This will facilitate microbial ecology research and expand our understanding of microbial processes and their ecological roles in extreme environments.

    Biodiversity and cold adaptive mechanisms of psychrophiles
    Yuhua Xin, Yuguang Zhou, Xiuzhu Dong
    Biodiv Sci. 2013, 21 (4):  468-480.  doi:10.3724/SP.J.1003.2013.13040
    Abstract ( 1731 )   HTML ( 0 )   PDF (364KB) ( 2868 )   Save
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    Cold-adapted bacteria and archaea are widely distributed in cold environments on Earth, such as permafrost, cold soils and deserts, glaciers, lakes, sea ice in the Arctic, Antarctic and high mountains, as well as the deep sea, ice caves and the atmospheric stratosphere etc. Cold-adapted organisms inhabiting these environments exhibit rich diversity. Studies on the biogeography of psychrophiles will enable us to understand their biodiversity, distribution and origins. Due to long-term living in cold regions, cold-adapted bacteria and archeae have developed specific physiological mechanisms of adaptation to cold environments. These mechanisms include: regulating the fluidity of the cytoplasmic membrane through adjusting the composition of membrane lipids; achieving low-temperature protection through compatibility solute, antifreeze proteins, ice-binding proteins, ice-nucleation proteins and anti-nucleating proteins; production of heat-shock and cold- shock proteins, cold acclimation protein and DEAD-box RNA helicase at low temperatures; production of cold-active enzymes; increasing energy generation and conservation. With the rapid development of sequencing technology, various omics-based approaches have been used to reveal cold-adaptive mechanisms of psychrophiles at the genomic level.

    Antibiotic resistance genes in the environment
    Jianqiang Su, Fuyi Huang, Yongguan Zhu
    Biodiv Sci. 2013, 21 (4):  481-487.  doi:10.3724/SP.J.1003.2013.07071
    Abstract ( 2385 )   HTML ( 1 )   PDF (352KB) ( 5206 )   Save
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    Antibiotic resistance and its spread in bacteria are topics of great importance in global research. In this paper, we review recent progress in understanding sources, dissemination, distribution and discovery of novel antibiotics resistance genes (ARGs) in the environment. Bacteria exhibiting intrinsic resistance and antibiotic resistant bacteria in feces from humans and animals are the major sources of ARGs occurring in the environment. A variety of novel ARGs have been discovered using functional metagenomics. Recently, the long-term overuse of antibotics in drug therapy and animal husbandry has led to an increase in diversity and abundance of ARGs, causing the environmental dissemination of ARGs in aquatic water, sewage treatment plants, rivers, sediment and soil. Future research should focus on dissemination mechanisms of ARGs, the discovery of novel ARGs and their resistant mechanisms, and the establishment of environmental risk assessment systems for ARGs.

    Distribution pattern and maintenance of ectomycorrhizal fungus diversity
    Cheng Gao, Liangdong Guo
    Biodiv Sci. 2013, 21 (4):  488-498.  doi:10.3724/SP.J.1003.2013.11055
    Abstract ( 1747 )   HTML ( 0 )   PDF (301KB) ( 3138 )   Save
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    Ectomycorrhiza (ECM) are symbionts formed between soil fungi and plant root systems, in which the fungus exchanges soil-derived nutrients for carbohydrates obtained from the host plant. As an important component of terrestrial ecosystems, ECM fungi can play an essential role in biodiversity maintenance and plant community succession. Understanding the distribution pattern and maintenance of ECM fungal diversity is therefore critical to the study of biodiversity and ecosystem functioning. An analysis of results of recent research indicates that ECM fungal diversity increases with increasing latitude, i.e. from tropical to subtropical and temperate regions. The role of dispersal in ECM fungal distribution is dependent on spatial scale. Thus, it has been found to be weak across global and local scales, but strong at regional and small scales. At the local scale, its influence has also been shown to be host-dominant dependent; thus, it is important in host non-dominant ecosystems, but not in host dominant ecosystems. Selection by plant, animal, microbe and abiotic factors can also affect the distribution pattern of ECM fungi, according to studies of temperate ecosystems. In contrast, studies of tropical ecosystems indicate that selection on ECM fungal distribution can be either strong or weak. ECM fungal diversity is also influenced by plant diversity and productivity. The plant diversity hypothesis at host genus-level fits well with ECM fungal diversity in temperate, subtropical and tropical forest ecosystems; in contrast, the productivity diversity hypothesis is only supported by some studies in temperate forest ecosystems. We propose that future studies should focus on the distribution pattern, maintenance mechanism and ecosystem function of ECM fungal diversity at a global scale, taking account of scenarios of global climate change.

    Chinese polypore diversities: species, mycota and ecological functions
    Liwei Zhou, Yucheng Dai
    Biodiv Sci. 2013, 21 (4):  499-506.  doi:10.3724/SP.J.1003.2013.08074
    Abstract ( 1435 )   HTML ( 0 )   PDF (537KB) ( 2474 )   Save
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    Polypores are the group of macro-basidiomycetes with poroid hymenophore and corky basidiocarps that mainly grow on wood. China contains multiple climatic zones and geographic topographies, and thus possesses a variety of forest and vegetation types that provide rich habitats for polypores. Based on extensive collections conducted over a long period of time, a considerable knowledge of Chinese polypore species has been obtained, and this has been enriched further in recent years by using molecular technology. China possesses the highest polypore diversity in the world and 704 polypore species, belonging to 134 genera, 22 families and 11 orders, have been recorded within its borders. These 704 species are composed of cosmopolitan, boreal/temperate and tropical-subtropical elements. White-rot polypores are considered as potential industrial resources, while brown-rot polypores play an essential role in forest renewal.

    Myxomycete diversity in hilly forests of East China
    Qun Dai, Shuzhen Yan, Huiqin Yao, Shuanglin Chen
    Biodiv Sci. 2013, 21 (4):  507-513.  doi:10.3724/SP.J.1003.2013.07028
    Abstract ( 1601 )   HTML ( 0 )   PDF (200KB) ( 2347 )   Save
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    We explored myxomycete species diversity in woodlands on Huangfu Mountain in Chuzhou of Anhui Province, Zijin Mountain in Nanjing of Jiangsu Province, representing the hilly forest ecosystems of East China. Three sample plots of coniferous forest and broad-leaved forests were examined on each mountain. The results showed that a total of 58 myxomycete species belonging to 21 genera of 10 families in 5 orders were found. 41 species belonging to 17 genera of 9 families in 5 orders present on Huangfu Mountain, 27 species including Licea punctiformis, Cribraria tenella and Perichaena corticalis were newly recorded species for Anhui, and 51 species belonging to 20 genera of 10 families in 5 orders occurred on Zijin Mountain, 35 species including Licea pedicellata, Cribraria intricata and Calomyxa metallica were newly recorded species for Jiangsu. The species Clastoderma debaryanum and Arcyria cinerea were the most common species on both mountains with relative abundances of 32.72% vs. 30.59% and 21.27% vs. 26.30%, respectively. It was also evident that Liceales and Stemonitales were more frequent in coniferous forests, while Trichiales and Physarales were more frequent in broad-leaved forests. Both species diversity index and numbers of species of myxomycetes were more higher in broad-leaved forests than in coniferous forests. Interestingly, the similarity of myxomycete species compositions between the two mountains was 68.57% for broad-leaved forests and 59.57% for coniferous forests and both of these values were higher than those based on comparisons between broad-leaved and coniferous forests within each mountain system. Thus, forest type has a greater effect on species composition of myxomycetes than distance between mountains.


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