Abstract:

Abstract:[Objective] To obtain and characterize a versatile strain isolated from the soil of Yellow River Delta. [Methods] The strain was isolated by anaerobic technologies and identified by sequencing the 16S rRNA gene. The morphology was depicted with Gram staining and scanning electron microscope. High performance liquid chromatography and gas chromatography were used to analyze the metabolic substrates and productions. Ferric citrate (FeC₆H₅O₇), ferrihydrite (FeOOH) and magnetite (Fe₃O₄) were supplied to detect the capability of Fe(Ⅲ) reduction of this strain. Microbial fuel cells were constructed with graphite as electrodes to test the electrochemical activity of this strain. [Results] Compared to Clostridium bifermentans, the similarity of 16S rRNA gene is 97.99%. It is a rod, Gram-positive bacterium, which can use glucose to produce hydrogen, carbon dioxide, acetate and butyrate. The Fe(Ⅲ) reduction results showed that it could reduce soluble ferric citrate, amorphous ferrihydrite and crystal magnetite. Furthermore, the electrochemical activity was detected and the maximum current density peaked at 6.5 mA/m². [Conclusion] In this work, a versatile strain which is capable of producing hydrogen, electricity and reducing iron oxide, was successfully isolated from the soil of Yellow River Delta named as Clostridium bifermentans EZ-1.

Abstract:[Objective] To explore the effect of photoelectron and photogenerated hole on the metabolites of Alcaligenes faecalis. [Methods] We compared different effect of photoelectron and photogenerated hole on metabolism of Alcaligenes faecalis through the Three-dimensional fluorescence spectroscopy by adding the hole scavenger and electron capturer. [Results] Under light, the hole scavenger group obviously produced 4 to 5 times higher humus-like substances and intensity of NADH fluorescence peaks than the electron capturer group, while the Three-dimensional fluorescence spectra did not show visible change among the experimental sets under dark. In contrast, the electron capturer group under light shows stronger fluorescence peak than under dark. [Conclusion] This is the first report that the photoelectron will promote the Alcaligenes faecalis to produce humus substances and more energy. The photogenerated hole will promote the Alcaligenes faecalis to produce protein.

Abstract:Microorganisms are important driver for the circulation of biogeochemical elements and play a vital role in the redox of metal elements possessing variable valence such as manganese. In recent years, the discovery and wide distribution of Mn(Ⅲ) in certain environment enrich our knowledge of natural manganese cycle. Some reports showed that geochemical cycling of manganese, especially dissimilatory manganese reduction, was closely related to microbial extracellular electron transfer, and dissimilatory manganese reduction involves five mechanisms of extracellular electron transfer. In this review, we discuss geochemical cycling and significance of manganese; microbial diversity of manganese cycle involving three aspects:mechanisms of microbial extracellular electron transfer, manganese oxidation mediated by microorganisms and manganese reduction mediated by microorganisms; The environmental significance of microbial geochemical manganese cycle. The research on the process of manganese cycle not only enriches related theories, but also stimulates the development of application including biological manganese removal, in-situ remediation of contaminants and bioleaching.

Abstract:Bioleaching is to extract valuable metals from their ores by microbial metabolic activity to take iron/sulfur. Microbial metabolic diversity and coupling function networks in metallurgical systems, especially functional networks dominated by iron and sulfur metabolism, play a major role in driving and accelerating the dissolution process of sulfide ore. Therefore, it is the core research area on bio-metallurgy technology. We summarize here the microbial diversity and iron/sulfur metabolism pathways in the metallurgical system, as well as the interactions between microbial metabolism diversity and minerals from the perspectives of metabolic coupling functional network.

Abstract:[Objective] To explore the mineralogical, chemical and microscopic properties of extracellular vivianite formation induced by iron-reducing bacteria Shewanella oneidensis MR-4. [Methods] MR-4 cells grown with 30 mmol/L of lactate and 10 mmol/L of amorphous ferrihydrite, which were used as electron donor and electron acceptor, respectively. The medium was buffered with 30 mmol/L[HCO₃^-] and 5 mmol/L[PO₄^3-], and the culture was incubated at 30℃. The headspace of serum bottle flushed with N₂/CO₂(V/V, 80/20). The pH, biomass and[Fe(Ⅱ)] of the culture were measured by sampling at different time points. Meanwhile, the combination of X-ray diffraction, scanning electron microscope, laser Raman and transmission electron microscope approaches were applied to characterize the mineralogical, chemical and morphological properties of products produced within the culture. [Results] MR-4 could couple the reduction of Fe(Ⅲ) with the oxidation of lactate for their cell growth and mineral transformation of Ferrihydrite. Specifically, ferrihydrite was initially transformed to nanometer-sized magnetite particles and majorly to micrometer-sized vivianite with bladed and fibrous morphologies finally. [Conclusion] The biomineralization process and products by MR-4 were strongly affected by environmental conditions such as the types and concentration of anions. In this case with relatively high[PO₄^3-] within the culture, ferrihydrite was initially converted to nanometer-sized magnetite, and was transformed into vivianite dominantly at the end of the culture. The result of this paper provides a new insight for comprehensive understanding of the microbial induced biomineralization of iron-reducing bacteria and its role in the iron element biogeochemical cycle.

Abstract:[Objective] To explore the composition and diversity of sulfur-oxidizing bacteria (SOB) community and its response to environmental variables in the mainstream and branches of the Three Gorges Reservoir (TGR). [Methods] A total of nine sampling locations were selected along the mainstream and branches of the TGR in March 2017. The physical and chemical parameters were measured on the sampled waters, followed by soxB gene-based phylogenetic analyses. The correlation analysis was performed between the physicochemical properties of the sampled waters and the composition and diversity of sulfur-oxidizing bacterial community. [Results] SOB in the collocted TGR waters belonged to α-Proteobacteria and β-Proteobacteria, with the the latter being dominant (relative abundance was higher than 95.6% in the studied mainstream and branch samples). Cluster analysis and principal coordinate analysis (PCoA) showed that the branch samples are scattered with each other and with their corresponding mainstream sample, while the mainstream sampls are relatively more centralized. The Mantel test showed that the SOB population composition was significantly (P < 0.05) correlated with the measured physicochemical parameters (i.e. water temperature, salinity, dissolved oxygen, algal content and pH) of the water samples. Pearson correlation analysis showed that the community diversity of sulfur-oxidizing bacteria was negatively correlated with algal content and dissolved inorganic carbon (DIC). [Conclusion] The SOB in the branch and mainstream TGR waters mainly belongs to the Proteobacteria. The composition of the SOB populations is similar among the mainstream samples, whereas the SOB population composition in the branch samples differs with each other and with their corresponding mainstream samples. This situation is mainly caused by the characteristic physical and chemical properties of the TGR waters.

Abstract:Estuarine ecosystems are characterized by extreme variations of salinity and nutrients. In such ecosystems, mechanisms of matter cycling are highly complex. Apart from the influences of fresh and marine water, and interaction between land and ocean, bacterioplankton also plays an important role in the matter cycling in estuarine aquatic ecosystems. Studies on bacterioplankton are, therefore, considered important for the understanding of matter cycling in the subtropical estuary such as that of the Pearl River Estuary. Previous studies in Pearl River Estuary show that the most dominant bacterioplankton groups were Proteobacteria and Cyanobacteria. While the bacterial community structure and abundance were influenced by salinity, temperature and nutrient concentration, their productions and abundance were limited by virus and flagellate, and there was positive relationship between bacterial biomass and phytoplankton. However, there were no comprehensive studies about function and cycle of earth matter of bacteria in Pearl River Estuary. Knowledge gaps still exist about mechanism for transformation of organic matter driven by microorganism and the corresponding ecological significance in this region. This review covers studies on estuarine bacterioplankton species composition, distribution, biomass, matter cycling and other relative environmental factors. Additionally, this article provides a future framework for Pearl River Estuary aquatic ecological system.

Abstract:Mangrove ecosystem is indispensable in maintaining biodiversity and removing pollutants to keep the ecological balance of coastal zone. Archaea, ubiquitous in mangrove sediments, play an important role in the biogeochemical cycles of elements. Archaea possess carbon metabolic versatility by fixing CO₂, participating in the methane cycle, producing acetic acid, and degrading proteins, carbohydrates and other organic matter. However, knowledge about metabolism of archaea in mangrove sediments is still lacking. Rapid development of high-throughput sequencing technology has promoted the discovery of a variety of new archaea phyla, indicating various metabolic potentials in carbon metabolism. This review briefly outlined the main phyla of archaea and their geographical distribution, summarized the latest advances on understanding of carbon metabolic versatility by archaea, and highlighted the ecological patterns and functional traits of these archaea in mangrove ecosystems, providing a foundation for further research on the more detailed metabolic mechanisms of archaea.

Abstract:Wetland is one of the largest carbon sink among all terrestrial ecosystems, and regarded as the main emission source of methane (CH₄) in the atmosphere. As CH₄ has 34 times warming potential of carbon dioxide (CO₂)per mole, it is of great importance to study the contribution of wetland as carbon sink or carbon source to global climate change. Totally, 80% to 90% of CH₄ emissions come from microbial activity, and CH₄ flux in wetland is closely related to microbial composition, abundance and function of methanogens and methanotrophs. However, the studies on the effects and mechanisms of the functional microorganisms that control CH₄ cycling in wetland ecosystem is relatively decentralized. To better understand the microbial regulation mechanism of CH₄ emission process, we provide an overview of microbial community associated to CH₄ cycling, the factors influencing the microbial methane emission activity, and the microbial methane emission mechanisms in wetland ecosystem. Besides, we indicate further research needs on microbial-driven CH₄ emission and their potential response to climate change.

Abstract:Coastal wetlands are ecosystems between terrestrial and marine ecosystems, which are highly diverse and also result in highly diverse microbial communities. In the last several decades, an increasing nitrogen load into coastal wetland ecosystems causes serious environmental problems such as eutrophication, and harmful algal blooms. Here we review the microbial communities involved in nitrogen cycling processes, such as nitrogen fixation, nitrification, denitrification, anaerobic ammonium oxidation, dissimilatory nitrate reduction to ammonium processes, and their key functional genes including nifH, amoA, hzo, nirK, nirS and nrfA as well as related environmental factors to further understand the microbially-driven nitrogen cycling processes for potentially removing nitrogen to mitigate eutrophication and harmful algal blooms.

Abstract:Microorganisms are the dominant players driving the nitrogen cycles in hot springs. Thus, exporing microbial community composition of nitrogen-related microorganisms and their ecological response to environmental factors are of important theoretical and practical value for the study of biogeochemical cycling of nitrogen, life evolution and bioremediation. This review focuses on the distribution of functional microorganisms involved in the nitrogen cyclings and how their functional gene abundance and activity responded to environmental factors (e.g., temperature, pH). So far, microbial functional groups that have been investigated in hot springs included nitrogen-fixation, aerobic (anaerobic) ammonia oxidation and denitrification. Finally, prospect was given on the microbial studies on nitrogen cycles in hot springs.

Abstract:[Objective] This study is aimed to investigate the interaction effects of marine free-living nematodes and microbes on carbon and nitrogen cycles in coastal sediments. [Methods] We used 16S rRNA and 18S rRNA high-throughput sequencing technology to inspect the diversity and community of bacteria, archaea and eukaryotes in 33 coastal sediment samples. The Spearman correlation method was adapted to analyze the co-occurrence pattern between marine nematodes and microbes (bacteria and archaea), to recognize the microbial group with significant correlation with nematodes. [Results] In summer, the average relative abundance of nematode OTUs decreased with the increasing depths both in mangrove and intertidal mudflat sediments. Similar pattern was discovered in winter samples with one exception that the averaged relative abundance of nematode OTUs in deeper layer was significantly higher than that in upper layer. The five most abundant marine nematode OTUs belong to Monhysterida (47%), Chromadorida (19%), Enoplia (16%) and Tylenchida (9%). Those OTUs are significantly correlated with Thermoplasmata, Bathyarchaeota, gamma-and delta-Proteobacteria. [Conclusion] In the wetland sediments sampled from Mai Po Nature Reserve of Hong Kong, the microbes those have significant correlation with nematodes play important roles in carbon, nitrogen and sulfur cycles. It implies that the potential interaction effects between marine nematodes and microbes have crucial impacts on biogeochemical cycles. Our results could help us to uncover the ecological function of nematodes in the environments, to better understand the roles of marine nematodes in the benthic ecosystems.

Abstract:[Objective] To understande the role of microbes for carbon cycling in acid mine drainage (AMD) system. [Methods] The 16S rRNA high-throughput sequencing, PICRUSt functional prediction method and functional gene chip technology were used to analyze the microbial community composition and functional gene composition in the two systems of leaching heap (LH) and leaching solution (LS) in Dexing Copper Mine. [Results] Both functional gene array and functional prediction analysis show that there were significant differences in the carbon cycle genes between LH and LS (P < 0.05). Besides, the carbon fixation genes related to Calvin cycle and reductive tricarboxylic acid cycle, and carbon degradation genes related to hemicellulose and cellulose degradation were both higher in LS than LH. The differences were caused by environmental condition, especially for contents of TON, Ca, ES, Fe³⁺ and P. [Conclusion] In the extremely acid environment, differences in environmental condition can screen for different carbon cycling genes. Then, the categories of microbies participating in the main carbon cycling process would decrease in leaching solution, while the relative abundance would increase, and eventually change the carbon cycling pattern.

Abstract:[Objective] The mixed methanogenic flora with high methane production from Baiyinhua lignite was obtained from several coalmines and an anaerobic polluted water processing tank by enrichment, mixture and domestication. The community structure was analyzed and its methane production condition from lignite was optimized. [Methods] The community structure was analyzed by Miseq high-throughput sequencing. Plackett-Burman and Box-Behnken tests were conducted to screen and optimize the main factors influencing the efficiency of methane production. [Results] The mixed flora (HN+MD+WT) combined with indigenous and exogenous microbial culture produced the highest methane after domestication. The diversity of bacterial community was abundant, in which the dominant portion was Desulfovibrio (belong to proteobacteria, 15.07%), Macellibacteroides (belong to bacteroidetes, 14.6%), Clostridiaceae (belong to Firmicutes, 9.77%), Dethiosulfovibrio (belong to Synergistetes, 8.76%) and Oceanotoga (belong to thermotogae, 8.66%). All the archaea were assigned to Euryarchaeota, and its diversity was single comparatively. Methanocalculus (80.28%) was the most dominant genus. Plackett-Burman test results indicated temperature, concentrations of CoCl₂and NiCl₂ were the most important influencing factors. Box-Behnken test results showed that the optimal conditions were as follows:temperature 36℃, CoCl₂ concentration 0.17 g/L, NiCl₂ concentration 0.02 g/L, under which the methane accumulation is up to 159.3 μmol/g (20 d). [Conclusion] A mixed flora with high methane production could be obtained by domestication. The productivity of methane could be enhanced significantly by optimizing the culture condition.

Abstract:Shale gas is the natural gas locked within the shale formation. It is estimated that 1/3 of natural gas is shale gas. Shale gas is found mainly in China, North America, and Russia. Hydraulic fracturing is a commonly used method to recover shale gas, which affects greatly on deep subsurface microorganisms. The microbial communities vary at different stages of hydraulic fracturing. Among them, methanogen may improve shale gas production, while the acid-producing bacteria that could corrode the equipment, may lower the gas production. With the aim of studying shale gas extraction and deep subsurface microbial interactions as well as improving extracting shale gas, this review focuses on current understandings of shale gas extraction and its impacts on deep subsurface microorganisms.

Abstract:The majority of microbial species in the environment remains uncultivated, called uncultivated microorganisms or microbial "dark matter". Unraveling the mysteries of these microbial "dark matter" is especially important to understand the diversity of microbes and their metabolic characteristics. These data can provide insights into the microbes involved in ecological processes, and insights into the early diversification of microbial lineages and the evolution of Bacteria and Archaea. DNA genome sequences of microbial "dark matter" could be recovered from the environment samples by population binning of metagenomics and single-cell genomics, independently or combined synergistically. The metabolic potential could be predicted based on bioinformatics analysis. In this mini-review, we briefly introduce the methods and challenges in this area, summarize the main groups of microbial "dark matter" that has been explored, and indicate the future research opportunities.

Abstract:[Objective] RNA extraction is considered the key for soil metatranscriptomics and it is expected that different methods would have generated distinct resolution of active soil microbiome. However, it remains largely unknown about the quantitative bias assessment of soil microbial communities associated with commercial Kits RNA (KR) and Manual RNA extraction (MR) methods. The aim of this study was to assess the bias of metatranscriptomics associated with total RNA extractions by commercial kits and manual methods from three geographically distinct paddy soils. [Methods] Three kinds of paddy soils were collected, representing distinctly different origin of parent materials including viscous black sand in Hailun city of Heilongjiang province, sandy loam in Binhai city of Jiangsu province, quaternary red clay in Yingtan city of Jiangxi province. Total RNA was obtained by commercial kit method and manual methods. The quantity and quality of total RNA were assessed by ultraviolet spectrophotometry and agarose gel electrophoresis. The abundance and composition of soil microbiome was analyzed by real-time quantitative PCR and high-throughput sequencing of cDNA reversely transcribed from 16S rRNA. [Results] The purity of RNA extracted by kit method was higher than that of manual method, but it did not hold true for the quantity of RNA extracts. The kit method generated higher quantity of soil RNA extract from paddy soils with higher organic matters from Heilongjiang and Jiangsu provinces, while the manual MR method recovered more RNA from paddy soil in Yingtan city of Jiangxi province with lower organic matter. High-throughput sequencing revealed a total of 27 phyla and 409 genera in three paddy soils, and 19 phyla and 181 genera were statistically significantly biased, i.e., the significant difference in relative abundance of these phylotypes was observed between manual MR and kit KR methods. These 19 phyla and 181 genera averaged for 40.4% and 44.4% of the total microbial abundance in soils. There are 11 phyla with higher relative abundance by KR than MR methods, and it is noteworthy that only Armatimonadetes phylum was KR-specifically biased, i.e., it is consistently detected in three soils with higher abundance by KR than MR methods. Similarly, the MR method also led to higher abundance of 11 phyla than KR method, and the Firmicutes is the only phylum for MR-specific bias, i.e., it is consistently observed with higher abundance in three soils by MR than KR method. At the genus level, the kit method consistently revealed two genera with higher relative abundance in all three paddy soils than manual method, and five genera were preferentially recovered by MR method in all three soils. We further assessed a total of 72 numerically dominant genera that could be recovered from all three soils having a relative abundance > 0.1%. These genera accounted for more than 80% of total microbial abundance in the three soils. The result suggested that 48 out of 72 genera have the same changing patterns of relative abundance among three paddy soils regardless of KR and MR methods. For example, the manual RNA extraction method indicated that the relative abundance of aerobic methanotrophs could be arranged in a decreasing order as Heilongjiang (1.68%) > Jiangxi (0.90%) > Jiangsu (0.59%), while the kit KR RNA extraction method has the same order as Heilongjiang (0.52%) > Jiangxi (0.18%) > Jiangsu (0.13%). [Conclusion] Among 27 phyla and 409 genera detected in paddy soils, there are only 2 phyla and 7 genera that was consistently biased in all three paddy soils by either kits KR or manual MR methods. It suggests that the biased phylotypes associated with the RNA extraction method itself could be insignificant, accounting only for 7.4% and 1.7% of the total phyla and genera respectively. Although the quantity and quality of RNA extracted from paddy soil are obviously different between manual MR and kit KR methods, the bias associated with these two RNA extraction methods has no significant impact on the biogeographic patterns of soil microbiomes in the three paddy soil tested. It is estimated that 70% of phyla and 22% of genera detected were observed with statistically significant difference between KR and MR methods. However, both RNA extraction methods could lead to the same conclusions regarding the changing patterns in relative abundance of microbial phylotpes among the three paddy soil tested. Despite the fact that the detection of every individual phylotype cannot be entirely reproduced by both methods and there are huge difference between these two methods, it seems plausible that the difference among soil types is sufficiently large so that the recovery of microbial communities would not be biased by RNA extraction method itself. These results imply that the method-specific bias of phylotype detection is much less than expected during soil RNA extraction. For future study the choice of RNA extraction method may not be of significant help, and the priority is to have experimental manipulation and treatments that would select for microbiomes with difference significantly larger than the bias associated with RNA extraction methods.