Abstract:Microorganisms are widely distributed in various habitats of the earth, and their species diversity is tremendous. However, only a small portion of their representatives are cultivated with the current technology. Those microbes that are not cultivated under laboratory conditions are termed “uncultured microbes”. Uncutured microbes are the majority of the microbial diversity. This review summarizes the recently developed cultivation techniques for microorganisms, with focuses on techniques such as “dilute to extinction culture”, “high-throughput culturing”, “diffusion chambers”, “soil substrate membrane system”, and “single cell encapsulation”.

Abstract:To discover and characterize microbial members within their community and their roles in the environment, high-throughput omics approaches are being developed and applied. Among them, sequencing- and microarray-based metagenomics is the most mature key approach, providing information basis for most other omics technologies. Metatranscriptomics, metaproteomics and community metabolomics have had limited successes but already shown promising potentials. All of the omics approaches lie on the support of bioinformatics, which becomes a major bottleneck in omics applications. These new omics technologies are revolutionizing the field of environmental microbiology in revealing the genetic potentials and functional activities of microbial communities.

Abstract:The knowledge of microorganisms in ecological environments is already reached to the level of metabolic process study of microbial community with omics methods from the isolation dependent study. However, the normally used microbial community analysis method which is based on PCR amplification with “universal” primers would cause the “miss” of various microorganisms. Therefore, we need to seek some methods to find the “missed” microorganisms. Although there are critical limitations in cultivation of microorganisms, the modification of cultivation method to isolate novel types of microorganisms or enrich special functional microorganisms is still a useful method to increase the boundary of our knowledge. Based on the metagenome databases, we can analyze the coverage of “universal” primers and can also analyze the global patterns of different functional microorganisms. Because of high content of ribosomal RNA, modified metatranscriptome analysis will become a useful method for the simultaneous determination of active bacteria, archaea and microeukaryotes. Seeking “missed” microorganisms is an important research field to extend our knowledge about microorganisms and correctly understand different earth element cycles.

Abstract:Human activities introduced increased amounts of nitrogen in coastal oceans, causing eutrophication and numerous ecological and environmental problems. It is crucial to better illustrate and understand the function and contribution of the microbe-driving nitrogen cycle within the coastal ecosystems, especially under the global change background. This review focuses on the rates, fluxes, contribution and functional gene quantity of microbes in nitrogen fixation, ammonification, nitrification, denitrification, dissimilatory nitrate reduction to ammonium, and anammox in coastal sediments. The controls of major physiochemical and biological factors (e.g. temperature, dissolved oxygen, salinity, labile dissolved organic carbon, dissolved inorganic nitrogen, submerged?macrophytes and benthic animals) on these processes, as well as functionally related microbial groups and pathways (e.g. ammonia-oxidizing bacteria and archaea and nitrate reduction), are summarized.

Abstract:Deep-sea environment is typically under pressure where piezophiles are the dominant life-forms in such ecosystem. As the development of sampling and cultivation techniques, various piezophilic microorganisms have been isolated from deep-sea, including certain obligated piezophilic species which cannot grow under ambient pressure. Through previous systematic investigations on these piezophiles, the adaptation mechanism to elevated pressure has been partly revealed and some unique metabolites have been identified. Moreover, the research on piezophic microorganisms also helps us to better understand the limitation, origin and evolution of life. This review will focus on the diversity of piezophic microorganisms and their adaptation strategies, thereafter try to illustrate the important roles that the deep-marine microorganisms have been playing on the global geobiochemistry through historical record.

Abstract:The oceans are full of microorganisms, which play a significant role in global carbon cycle. Microbial carbon sequestration in the ocean, as a cutting-edge scientific issue, receives a great deal attention in the context of global climate change. Based on the microbial carbon pump conceptual framework, microbes are major producers of recalcitrant dissolved organic carbon (RDOC) that can stay in ocean water column for long time storage. Different microbial groups contribute to RDOC carbon pool in different ways. This paper addresses groups such as autotrophic and heterotrophic microorganisms, viruses and protozoa with respect to their various ecological characteristics and specific roles in RDOC formation.

Abstract:Lake is one of the major ecosystems on the earth. Lake ecosystems play an important role in the nutrient cycling in the regional as well as in the global scale due its connection with different interfaces and its functioning as a junction in the catchment. Microbes are key biological components of the lake ecosystems and are the major forces driving the cycling of nutrients including the carbon. Lake ecosystems particularly in shallow lakes always possess two alternative stable states, a turbid state dominated by phytoplankton and a clear state dominated by submersed macrophyte. Such a change of alternative states is always related to the loading of nutrients including phosphorus and nitrogen as a result of human activities and global change. The shift of alternative states has strong impacts on the ecosystem structure and its function. In this review, we focused on responses of microbial community structure under the regime shift between clear state and turbid state, and subsequently the change of microbial carbon cycling driven by the microbes in lakes. Based on these analyses, we further point out the major research priorities in this direction in the future. We hope such a review will be helpful for a better understanding on the carbon cycling and its mechanisms driven by microbes in lakes.

Abstract:Microorganisms are the engines driving the biogeochemical cycles of soil elements. The nitrogen cycle is one of the central processes of terrestrial ecosystems, and contains four main steps, i.e. nitrogen fixation, ammonification, nitrification, denitrification, all of which are driven by microorganisms. In the last decade, with the rapid development of culture-independent molecular techniques and high-throughput sequencing technologies, breakthrough progress has been made on the diversity and mechanisms of nitrifying microorganisms, and anaerobic ammonia oxidation (anammox) process and mechanisms. Here we review the available knowledge concerning the research progress in ammonia oxidation studies in China, and briefly introduce the researches on denitrifying microorganisms, anammox, and dissimilatory nitrate reduction to ammonium (DNRA), and then present the future perspectives on this research field. Novel techniques and methods will be applied to the future microbial ecology studies of soil nitrogen transformation. It needs to hold the frontiers of microbial ecology, in combination with significant demands for China’s sustainable agriculture, resources and environment protection, and global change research, primarily focusing on the following several areas: (1) to carry on investigations on the large-scale biogeographical patterns of soil nitrification processes and nitrifying microorganisms, and to elucidate the underlying mechanisms of spatial-temporal variations and their driving factors. (2) To explore the key microbe-meditated processes and mechanisms of nitrogen transformation, and link them to the relevant observations on gas flux (e.g. ammonia volatilization, N2O emissions) and reaction rates (e.g. the rates of mineralization and nitrification). (3) To elucidate the coupling between different nitrogen transformation processes in certain ecosystems, and to estimate the nitrogen balance and build models to predict nitrogen transformation and balance. These studies are expected to provide scientific basis for adjustment of nitrogen transformation processes, improvement of nitrogen utilization efficiency and elimination of its negative effects.

Abstract:Flooded rice field is one of major biogenic sources of greenhouse gas CH4. Complex organic matter is degraded to CH4 and CO2 by the co-operation of anaerobic microorganisms of several metabolic guilds involving the syntrophic oxidation of short-chain fatty acids like propionate, butyrate and acetate. Due to the fastidious nature of cultivation, the diversity and ecology of microorganisms involved in syntrophic oxidation in natural environments like paddy soils remain largely unexplored. Stable isotope probing (SIP), which links microbial identity and function, is a powerful tool to investigate the syntrophic oxidation of fatty acids in flooded paddy soils. This article reviews the recent research progresses in the thermodynamic principles, the interspecies interactions in the syntrophic oxidation of fatty acids, and paddy soils employing SIP technology. The knowledge acquired suggests that phylogenetically diverse bacterial groups are active in the syntrophic oxidation: except classic syntrophic bacteria, organisms belonging to uncultivated phylogenetic groups are also detected, which can serve as candidate syntrophs. Among archaea, Methanocella is the major methanogen partner in syntrophic oxidation of different fatty acids, indicating the importance of this group in CH4 production of paddy field soil.

Abstract:Climate warming is widely predicted to be largest and most rapid at high latitudes and high altitudes like Arctic tundra, alpine tundra, Tibetan plateau, etc. The impacts of climate change on these ecosystems are critical for the global C cycle because of the large amount of C stored in these cold regions. Microbes are key drivers in biogeochemical cycling, and microbial responses and feedbacks to climate change affect ecosystems functioning and stability. This paper review microbial community composition, diversity and spatial distributions in those cold ecosystems, and microbial responses to climate change (warming, nitrogen deposition, fire interference), which could provide base in expanding microbial community studies in cold ecosystems of China.

Abstract:Cold wetlands contribute great portion of the global methane. This is attributed to the inhabited diverse microbes including methanogenic archaea, where they convert the organic materials to methane. This review summarized the recent studies on the diversity of methanogenic archaea, and methane emission pathways in the cold wetlands and their correlation with environmental parameters. The so-far studies indicated that acetate is the main methanogenic precursor in the wetlands located in cold regions, hydrogenothophic methanogenesis occurs mainly in wetlands located in the warm regions and acidic peat, while methanol- and methyl amine-derived methanogensis restricts in ocean and saline water. Zoige wetland situates on Qinghai-Tibet Plateau locating in the low latitude region but at high altitude. Our previous study indicated the significant methanogenic contribution of methanol in this wetland. Accordingly, the methylotrophic and aceticlastic Methanosarcinales and hydrogenotrphic Methanomicrobiales constitute the predominant wetland archaeal community. However, methanogenic pathways and methanogen community structures vary with the wetland soil types and their pH as well as the vegetations, like methanol-derived methane accounting for 17% total methane flux in Eleocharis valleculosa growing soil, while acetate contribute the main methane in Carex muliensis planted soil in Zoige wetland. Though playing an important role in methane emission of cold wetlands, the so-far cultured cold-adaptive methanogenic strains are very few. The low-temperature-responsive genomics analyses show that a global gene reperpoire may involve in cold adaptation in methanogenic archaea.

Abstract:Soil microorganism, as a key decomposer, has a profound effect on carbon and nutrient cycling in terrestrial ecosystem. Through the decomposition process, microorganisms can return CO2 back to the atmosphere and release nutrients for plants. However, most of the previous study was conducted during the growing season, based on the assumption that microbial activity in frozen or snow-covered soils is negligible. Approximately 60% of the terrestrial earth surface experiences seasonal snow cover and seasonal soil frost. The recently published data has convincingly demonstrated that soil microbial activity in the field occurs at freezing temperatures, including arctic tundra, alpine tundra, boreal forests, wetlands and grasslands. The snow cover could effectively decouple soil temperatures from the atmosphere, resulting in higher soil temperatures; therefore, snow-covered soil microorganisms play important contribution to soil CO2 efflux and plant nutrient uptake. In this paper, we comprehensively analyzed the contribution of snow-covered soil microorganisms to soil carbon release and plant nutrient uptake. In addition, the present status in the research of snow-covered soil carbon and nitrogen cycling was overviewed. Furthermore, we raised major research areas in the future, emphasizing the importance and necessity to conduct the research concerning winter snow-covered ecological processes in tempeate areas.

Abstract:Mycorrhiza is a symbiotic association formed between soil fungi and plant roots. Mycorrhizal fungi exchange soil-derived nutrients for carbohydrates from host plants, and therefore play an important role in the cycle of carbon and nitrogen in ecosystems. Research results indicated that mycorrhizal fungi can obtain ca. 4%?26% of total net primary production of host plants, and biomass and secretion (glomalin) of mycorrhizal fungi are important soil carbon-pool. Simultaneously, mycorrhizal fungi may decompose the complex soil organic compounds. Nitrogen is transported from extraradical to intraradical hyphae by a transferring procedure from inorganic to organic and inorganic nitrogen in mycorrhizae. Advances of recent mycorrhizal researches on the metabolic function and mechanism of carbon and nitrogen were summarized and related fields in future studies were also mentioned in this review paper.

Abstract:The Gram-negative myxobacteria are phylogenetically located in the delta division of Proteobacteria. Myxobacteria are famous for their complicated multicellular behavior and excellent production ability of secondary metabolites, and are thus among important microbial resources for drug screening and of model organisms for the studies of prokaryotic intercellular communication, multicellular morphogenesis, and biological evolution. In this paper, we reviewed characteristics of myxobacteria and progresses related to their population diversity, ecological distribution, potential survival strategies and ecological functions.

Abstract:Microbially induced carbonate formation has attracted much attention in the field of geomicrobiology. Microorganisms have been demonstrated to be effective agents to produce polymorphy carbonate minerals by enhancing pH and CO32? concentration, both of which are the essential factors controlling the saturation index of carbonate minerals. Furthermore, microorganisms themselves and the secreted extracellular polymeric substances can also facilitate carbonate precipitation via serving as nucleation sites for mineral growth. Compared with abiotic carbonate minerals, microbially induced carbonate exhibits special properties on mineral morphology, trace elements content and carbon isotope composition. Understanding of microbially induced carbonate and their special signatures is of unequivocal significance to probe the microbial activities throughout the earth history and provide application to geologic CO2 sequestration. Here we reviewed the latest progress on microbially induced carbonate precipitation, the related microbe metabolism processes and, the differences between biogenic and chemogenic carbonate, possible application of microbially induced carbonate on microbialite and CO2 sequestration were discussed finally.

Abstract:Phototropy and chemotrophy microorganisms compose the whole microbe world. As non-phototrophic microorganisms are excluded from phototrophy due to the lack of phototropic system. Here we introduce a novel pathway of microorganism energy utilization. The non-phototrophic microorganisms could get solar energy through semiconducting mineral photocatalysis. In simulated system, under simulated solar light semiconducting minerals, such as metal oxides and metal sulfides, generated photo electrons which could be used by non-phototrophic microorganisms to support their metabolisms. The growth of microorganism was closely related to photon quantity and energy and the microorganism growth and mineral light absorption spectra were fitted well under different light wavelengths. The overall energy efficiency from photon to biomass was 0.13‰ to 1.90‰. Further studies revealed that in natural soil systems, semiconducting mineral photocatalysis could influence the microbial population. This study provided the evidence to reveal a novel but long existed pathway in which the semiconducting mineral photocatalysis could stimulate the non-phototrophic microorganism metabolisms.