青藏高原湖泊沉积物中有机碳组分构成及其对微生物群落结构的影响

【目的】探究湖泊沉积物中有机碳组分构成及其对湖泊微生物群落结构的影响。【方法】本研究采集了青藏高原29个湖泊共81个沉积物样品,通过硫酸水解法分析样品中易降解和难降解有机碳含量及其与环境变量之间的相关性;同时使用高通量测序技术分析样品中原核微生物和真菌群落的多样性和组成及其与易降解和难降解有机碳含量的相关关系。【结果】本研究的青藏高原湖泊沉积物中易降解有机碳Ⅰ(labile organic carbon Ⅰ, LOCⅠ)、易降解有机碳Ⅱ(labile organic carbon Ⅱ, LOCⅡ)和难降解有机碳(recalcitrant organic carbon, ROC)的含量分别为0.03–29.62 mg/g、0.02–23.38 mg/g和0.64–75.72 mg/g,ROC是沉积物有机碳的主要组分(占比为54.97%±19.50%)。LOCⅠ含量与海拔、总氮、总磷、钙离子、活性钙和活性铁含量显著相关(P<0.05);LOCⅡ含量与总氮、钙离子和活性钙含量显著相关;而ROC含量与海拔、总氮、总磷、钙离子和活性钙含量显著相关。其中,钙离子和活性钙的浓度与3种有机碳组分...     

Volatile halogenated organic compounds in European estuaries

Sources, sinks, and distribution patterns ofvolatile halogenated organic compounds (VHOC)in estuaries were investigated during 5 cruises within the BIOGEST programme. Due to their chemical and physical properties (e.g. toxicity, persistence, mobility) these compounds are of considerable environmental concern. A wide range of compounds has been identified and quantified generally ranging from 0.1 ng l^–1 to 350 ng l^–1. Insome samples extraordinarily high values up to4700 ng l^–1 were observed indicatingcontribution from anthropogenic sources.Generally, concentrations of halogenatedcompounds of anthropogenic origin dominatedthose of prevalent natural origin. Data ofselected VHOC are presented in relation tosalinity, particular organic carbon, and totalsuspended matter. Furthermore the observedconcentrations are compared with establishedwater quality regulations. Distributionpatterns of VHOC along the estuary indicatedcommon sources for specific halogenatedcompounds. Decreasing concentrations of mostVHOC along the estuary confirm that degassingto the atmosphere and dilution with sea waterare the dominating processes controlling thefate of these compounds in estuaries.     

Contrasted ecological niches shape fungal and prokaryotic community structure in mangroves sediments

Mangroves are forest ecosystems located at the interface between land and sea where sediments presented a variety of contrasted environmental conditions (i.e. oxic/anoxic, non-sulfidic/sulfidic, organic matter content) providing an ideal ecosystem to study microbial communities with niche differentiation and distinct community structures. In this work, prokaryotic and fungal compositions were investigated during both wet and dry seasons in New Caledonian mangrove sediments, from the surface to deeper horizons under the two most common tree species in this region (Avicennia marina and Rhizophora stylosa), using high-throughput sequencing. Our results showed that Bacteria and Archaea communities were mainly shaped by sediment depth while the fungal community was almost evenly distributed according to sediment depth, vegetation cover and season. A detailed analysis of prokaryotic and fungal phyla showed a dominance of Ascomycota over Basidiomycota whatever the compartment, while there was a clear shift in prokaryotic composition. Some prokaryotic phyla were enriched in surface layers such as Proteobacteria, Euryarchaeota while others were mostly associated with deeper layers as Chloroflexi, Bathyarchaeota, Aminicenantes. Our results highlight the importance of considering fungal and prokaryotic counterparts for a better understanding of the microbial succession involved in plant organic matter decomposition in tropical coastal sediments.     

Trophic diversity in the evolution and community assembly of loricariid catfishes

ABSTRACT: BACKGROUND: The Neotropical catfish family Loricariidae contains over 830 species that display extraordinary variation in jaw morphologies but nonetheless reveal little interspecific variation from a generalized diet of detritus and algae. To investigate this paradox, we collected delta13C and delta15N stable isotope signatures from 649 specimens representing 32 loricariid genera (82 species) from 19 local assemblages distributed across South America. We calculated vectors representing the distance and direction of each specimen relative to the delta15N/delta13C centroid for its local assemblage, and then examined the evolutionary diversification of loricariids across assemblage isotope niche space by regressing the mean vector for each genus in each assemblage onto a phylogeny reconstructed from osteological characters. RESULTS: Loricariids displayed a total range of delta15N assemblage centroid deviation spanning 4.9per thousand, which is within the tissue-diet discrimination range known for Loricariidae, indicating that they feed at a similar trophic level and that delta15N largely reflects differences in their dietary protein content. Total range of delta13C deviation spanned 7.4per thousand, which is less than the minimum range reported for neotropical river fish communities, suggesting that loricariids selectively assimilate a restricted subset of the full basal resource spectrum available to fishes. Phylogenetic regression of assemblage centroid-standardized vectors for delta15N and delta13C revealed that loricariid genera with allopatric distributions in disjunct river basins partition basal resources in an evolutionarily conserved manner concordant with patterns of jaw morphological specialization and with evolutionary diversification via ecological radiation. CONCLUSIONS: Trophic partitioning along elemental/nutritional gradients may provide an important mechanism of dietary segregation and evolutionary diversification among loricariids and perhaps other taxonomic groups of apparently generalist detritivores and herbivores. Evolutionary patterns among the Loricariidae show a high degree of trophic niche conservatism, indicating that evolutionary lineage affiliation can be a strong predictor of how basal consumers segregate trophic niche space.     

Molecular diversity and tools for deciphering the methanogen community structure and diversity in freshwater sediments

Methanogenic archaeal communities existing in freshwater sediments are responsible for approximately 50 % of the total global emission of methane. This process contributes significantly to global warming and, hence, necessitates interventional control measures to limit its emission. Unfortunately, the diversity and functional interactions of methanogenic populations occurring in these habitats are yet to be fully characterized. Considering several disadvantages of conventional culture-based methodologies, in recent years, impetus is given to molecular biology approaches to determine the community structure of freshwater sedimentary methanogenic archaea. 16S rRNA and methyl coenzyme M reductase (mcrA) gene-based cloning techniques are the first choice for this purpose. In addition, electrophoresis-based (denaturing gradient gel electrophoresis, temperature gradient gel electrophoresis, and terminal restriction fragment length polymorphism) and quantitative real-time polymerase chain reaction techniques have also found extensive applications. These techniques are highly sensitive, rapid, and reliable as compared to traditional culture-dependent approaches. Molecular diversity studies revealed the dominance of the orders Methanomicrobiales and Methanosarcinales of methanogens in freshwater sediments. The present review discusses in detail the status of the diversity of methanogens and the molecular approaches applied in this area of research.     

围栏对青藏高原不同类型草地土壤原核微生物多样性的影响

草地退化是草地植被的倒退演替,导致生物多样性丧失和生态系统功能退化,围栏是恢复退化草地生态系统功能的有效管理措施。微生物是土壤中的重要组成部分,在维持草地生态系统稳定性和功能方面发挥着重要作用。然而,目前尚不清楚围栏如何影响不同类型草地土壤微生物群落。以青藏高原草甸、草原和荒漠草地三种草地类型的退化草地为研究对象,设置围栏和放牧两种处理,采用Illumina HiSeq高通量测序技术研究了围栏对土壤原核微生物群落多样性和群落结构的影响。结果表明：围栏未显著影响草甸土壤原核微生物的丰富度、Shannon多样性和均匀度,但显著增加了草原土壤的原核微生物的丰富度、Shannon多样性和均匀度（P<0.05）,稍降低了荒漠草地土壤原核微生物的丰富度、Shannon多样性和均匀度（P=0.086、0.072和0.099）。在围栏处理的草地中,土壤原核微生物丰富度、Shannon多样性和均匀度与年均温、干旱度和pH显著负相关（P<0.01）,与年平均降水量、溶解性有机碳、地上生物量和植物多样性显著正相关（P<0.01）。在放牧处理的草地中,土壤原核微生物丰富度、Shannon多样性和均匀度与年均温和干旱度显著负相关（P<0.05）,但原核微生物丰富度和Shannon多样性与所有土壤理化和植被因素均无显著相关性。冗余分析（RDA）表明,不同类型草地土壤原核微生物群落结构发生了显著的变化,并沿草甸、草原和荒漠草地的过渡逐渐转变（P<0.001）。方差分解分析（VPA）进一步表明,原核微生物群落结构变化主要受年均温、年平均降水量、干旱度和pH的驱动。围栏显著改变了不同类型草地中部分样点土壤原核微生物群落结构。三种草地类型的主要原核微生物优势门均为放线菌门（Actinobacteria）、变形菌门（Proteobacteria）和酸杆菌门（Acidobacteria）。放线菌门（Actinobacteria）的相对丰度在荒漠草地土壤中最高,而变形菌门（Proteobacteria）和酸杆菌门（Acidobacteria）的相对丰度在草甸土壤中最高。此外,不同类型围栏和放牧草地土壤原核微生物类群的相对丰度均无显著差异。研究表明不同类型草地土壤原核微生物群落对围栏的响应不同,这为因地制宜制定草地管理措施提供了数据支持,为草地退化的防治提供了理论支持。     

功能多样性和谱系多样性对热带云雾林群落构建的影响

近年来, 功能多样性和谱系多样性为探究群落构建机制提供了新方法。为了更准确地了解海南岛高海拔热带云雾林群落构建机制, 该研究以海南岛霸王岭热带云雾林为对象, 测定7个环境因子和13个植物功能性状。利用主成分分析(PCA)筛选环境因子, 以霸王岭、尖峰岭和黎母山热带云雾林分布物种建立区域物种库, 结合模型, 分析Rao二次熵(RaoQ)和平均成对谱系距离(MPD)变化对植物群落构建的影响。结果表明: 林冠开阔度、土壤全磷含量和坡度是影响植物群落构建的关键环境因子。多数功能性状的系统发育信号很低且不显著, 说明热带云雾林群落的系统发育关系与功能性状随历史进程变化不一致。RaoQ和MPD的实际观测值都显著低于期望值, 且其标准效应值与土壤磷含量显著相关, 说明生境过滤是驱动热带云雾林群落构建的关键因子, 土壤磷含量是群落构建的关键环境筛。     

Diversity and distribution of the prokaryotic community in near-surface permafrost sediments in the Tianshan Mountains, China

The community structures and diversity of bacteria and archaea were investigated at 4 depths (1.5, 2.0, 2.5, and 3.0 m) in permafrost sediments in the Tianshan Mountains, using denaturing gradient gel electrophoresis of 16S rRNA gene amplified by polymerase chain reaction. Phylogenetic analysis of the dominant bands sequenced revealed the presence of rich diversity of bacteria, which could be related to the Proteobacteria, Actinobacteria, Acidobacteria, Gemmatimonadetes, Bacteroidetes, Firmicutes, and Chloroflexi. The Proteobacteria, consisting of the alpha, beta, gamma and epsilon subdivisions, were clearly the dominant group at all depths studied. Archaeal diversity was relatively low and archaeal 16S rRNA gene sequences were grouped into 3 phylogenetic clusters within the 2 kingdoms Euryarchaeota and Crenarchaeota. Within the Euryarchaeota, methanogen-related group II was most abundant at shallow depth (1.5 m), whereas halobacterium-related group I dominated at greater depths. The low-temperature Crenarchaeota group was detected only at 2.5 and 3.0 m. Specific-depth distribution of methanogen-related Euryarchaeota group II and denitrifying bacteria of the genus Pseudomonas dominated at 1.5 m depth, accompanied by a distinct peak in the ratio of NH4-N to NO3/NO2-N, implying the potential capacity of these organisms in near-surface permafrost to release the greenhouse gases N2O and CH4.     

Phylogenetic diversity and community assembly in a naturally fragmented system

We sought to assess effects of fragmentation and quantify the contribution of ecological processes to community assembly by measuring species richness, phylogenetic, and phenotypic diversity of species found in local and regional plant communities. Specifically, our fragmented system is Craters of the Moon National Monument and Preserve, Idaho, USA. CRMO is characterized by vegetated islands, kipukas, that are isolated in a matrix of lava. We used floristic surveys of vascular plants in 19 kipukas to create a local species list to compare traditional dispersion metrics, mean pairwise distance, and mean nearest taxon distance (MPD and MNTD), to a regional species list with phenotypic and phylogenetic data. We combined phylogenetic and functional trait data in a novel machine‐learning model selection approach, Community Assembly Model Inference (CAMI), to infer probability associated with different models of community assembly given the data. Finally, we used linear regression to explore whether the geography of kipukas explained estimated support for community assembly models. Using traditional metrics of MPD and MNTD neutral processes received the most support when comparing kipuka species to regional species. Individually no kipukas showed significant support for overdispersion. Rather, five kipukas showed significant support for phylogenetic clustering using MPD and two kipukas using MNTD. Using CAMI, we inferred neutral and filtering models structured the kipuka plant community for our trait of interest. Finally, we found as species richness in kipukas increases, model support for competition decreases and lower elevation kipukas show more support for habitat filtering models. While traditional phylogenetic community approaches suggest neutral assembly dynamics, recently developed approaches utilizing machine learning and model choice revealed joint influences of assembly processes to form the kipuka plant communities. Understanding ecological processes at play in naturally fragmented systems will aid in guiding our understanding of how fragmentation impacts future changes in landscapes.     

Evolutionary trends in the prokaryotic community and prokaryotic community-phage systems

The Evolutionary Constructor software has been used for computer simulation of the life and evolution of communities of unicellular haploid organisms (prokaryotic cells). Opposite trends of the community evolution (simplification and complication of the genome) have been studied. It has been demonstrated that species with reduced genomes tend to replace genetically and metabolically rich species under highly favorable environmental conditions. Under unfavorable conditions, the opposite tendency is observed. It has also been shown that introduction of phages capable of killing the cells into the system may radically change the current evolutionary trend.     

Towards revealing the global diversity and community assembly of soil eukaryotes

Soil fungi, protists, and animals (i.e., the eukaryome) play a critical role in key ecosystem functions in terrestrial ecosystems. Yet, we lack a holistic understanding of the processes shaping the global distribution of the eukaryome. We conducted a molecular analysis of 193 composite soil samples spanning the world's major biomes. Our analysis showed that the importance of selection processes was higher in the community assemblage of smaller-bodied and wider niche breadth organisms. Soil pH and mean annual precipitation were the primary determinants of the community structure of eukaryotic microbes and animals, respectively. We further found contrasting latitudinal diversity patterns and strengths for soil eukaryotic microbes and animals. Our results point to a potential link between body size and niche breadth of soil eukaryotes and the relative effect of ecological processes and environmental factors in driving their biogeographic patterns.     

Volatile organic compounds with characteristic odor in bamboo vinegar

Bamboo vinegar solutions had pHs of 2.5 to 2.8, and the amounts of organic constituents were estimated to be 2.3 to 4.6% (w/w). Volatile organic compounds (28 components) were detected by GC-MS, and among of these, 11 compounds were common to three samples of bamboo vinegar. Perhaps acetic acid, 3-methyl-1,2-cyclohexadione, guaiacol, p-cresol, and syringol contributed to the characteristic odors (sour, smoky, and medicinal note) in bamboo vinegar.     

Characterization of the prokaryotic diversity through a stratigraphic permafrost core profile from the Qinghai-Tibet Plateau

Permafrost on the Qinghai-Tibet Plateau is one of the most sensitive regions to climate warming, thus characterizing its microbial diversity and community composition may be important for understanding their potential responses to climate changes. Here, we investigated the prokaryotic diversity in a 10-m-long permafrost core from the Qinghai-Tibet Plateau by restriction fragment length polymorphism analysis targeting the 16S rRNA gene. We detected 191 and 17 bacterial and archaeal phylotypes representing 14 and 2 distinct phyla, respectively. Proteobacteria was the dominant bacterial phylum, while archaeal communities were characterized by a preponderance of Thaumarchaeota. Some of prokaryotic phylotypes were closely related to characterized species involved in carbon and nitrogen cycles, including nitrogen fixation, methane oxidation and nitrification. However, the majority of the phylotypes were only distantly related to known taxa at order or species level, suggesting the potential of novel diversity. Additionally, both bacterial α diversity and community composition changed significantly with sampling depth, where these communities mainly distributed according to core horizons. Arthrobacter-related phylotypes presented at high relative abundance in two active layer soils, while the deeper permafrost soils were dominated by Psychrobacter-related clones. Changes in bacterial community composition were correlated with most measured soil variables, such as carbon and nitrogen contents, pH, and conductivity.     

Biodegradation of organic compounds in vadose zone and aquifer sediments.

The microbial processes that occur in the subsurface under a typical Midwest agricultural soil were studied. A 26-m bore was installed in November of 1988 at a site of the Purdue University Agronomy Research Center. Aseptic collections of soil materials were made at 17 different depths. Physical analysis indicated that the site contained up to 14 different strata. The site materials were primarily glacial tills with a high carbonate content. The N, P, and organic C contents of sediments tended to decrease with depth. Ambient water content was generally less than the water content, which corresponds to a -0.3-bar equivalent. No pesticides were detected in the samples, and degradation of added 14C-labeled pesticides (atrazine and metolachlor) was not detected in slurry incubations of up to 128 days. The sorption of atrazine and metolachlor was correlated with the clay content of the sediments. Microbial biomass (determined by direct microscopic count, viable count, and phospholipid assay) in the tills was lower than in either the surface materials or the aquifer located at 25 m. The biodegradation of glucose and phenol occurred rapidly and without a lag in samples from the aquifer capillary fringe, saturated zone, and surface soils. In contrast, lag periods and smaller biodegradation rates were found in the till samples. Subsurface sediments are rich in microbial numbers and activity. The most active strata appear to be transmissive layers in the saturated zone. This implies that the availability of water may limit activity in the profile.     

A non-phylogenetic alpha diversity approach on prokaryotic community structure in aquatic systems

Comparative analyses of accumulating phylotype-abundance data of prokaryotic communities are relatively scarce and mainly approached with phylogenetic methodologies. However, when a great fraction of phylotypes is captured within a sample, application of alpha diversity measures is also possible, enabling the exploration of structural changes in prokaryotic communities. In the present study, phylotype-abundance data of Archaea and Bacteria were compiled from previous works on freshwater, thermal springs, and submarine mud volcanoes in Eastern Mediterranean region. Samples within each environment were used as pseudo-replicates to enable comparisons between the two assemblages (Archaea and Bacteria) and among different environments whereas sampling effort was found similar among samples using rarefaction curves. Phylotypes were defined as 16S rRNA sequences with 98% similarity. The most common diversity indices were calculated and relative abundance distributions (RADs) were employed to provide a more detailed interpretation of observed diversity patterns. The freshwater and mud volcanoes environments were the most diverse with respect to Bacteria but the least diverse considering Archaea, whereas thermal springs yielded very similar diversity for both assemblages. Overall, bacterial diversity was higher than archaeal with respect to richness and evenness since Archaea were characterized by high dominance and phylotype-poor distributions. The present comparative analysis of alpha diversity may offer useful insights into ecological processes shaping prokaryotic community structure, however equal sampling effort among different environments must be verified prior to analysis.     

Biodegradation of organic compounds in vadose zone and aquifer sediments.

The microbial processes that occur in the subsurface under a typical Midwest agricultural soil were studied. A 26-m bore was installed in November of 1988 at a site of the Purdue University Agronomy Research Center. Aseptic collections of soil materials were made at 17 different depths. Physical analysis indicated that the site contained up to 14 different strata. The site materials were primarily glacial tills with a high carbonate content. The N, P, and organic C contents of sediments tended to decrease with depth. Ambient water content was generally less than the water content, which corresponds to a -0.3-bar equivalent. No pesticides were detected in the samples, and degradation of added 14C-labeled pesticides (atrazine and metolachlor) was not detected in slurry incubations of up to 128 days. The sorption of atrazine and metolachlor was correlated with the clay content of the sediments. Microbial biomass (determined by direct microscopic count, viable count, and phospholipid assay) in the tills was lower than in either the surface materials or the aquifer located at 25 m. The biodegradation of glucose and phenol occurred rapidly and without a lag in samples from the aquifer capillary fringe, saturated zone, and surface soils. In contrast, lag periods and smaller biodegradation rates were found in the till samples. Subsurface sediments are rich in microbial numbers and activity. The most active strata appear to be transmissive layers in the saturated zone. This implies that the availability of water may limit activity in the profile.     

Hydrodynamic disturbance controls microbial community assembly and biogeochemical processes in coastal sediments

The microbial community composition and biogeochemical dynamics of coastal permeable (sand) sediments differs from cohesive (mud) sediments. Tide- and wave-driven hydrodynamic disturbance causes spatiotemporal variations in oxygen levels, which select for microbial generalists and disrupt redox cascades. In this work, we profiled microbial communities and biogeochemical dynamics in sediment profiles from three sites varying in their exposure to hydrodynamic disturbance. Strong variations in sediment geochemistry, biogeochemical activities, and microbial abundance, composition, and capabilities were observed between the sites. Most of these variations, except for microbial abundance and diversity, significantly correlated with the relative disturbance level of each sample. In line with previous findings, metabolically flexible habitat generalists (e.g., Flavobacteriaceae, Woeseaiceae, Rhodobacteraceae) dominated in all samples. However, we present evidence that aerobic specialists such as ammonia-oxidizing archaea (Nitrosopumilaceae) were more abundant and active in more disturbed samples, whereas bacteria capable of sulfate reduction (e.g., uncultured Desulfobacterales), dissimilatory nitrate reduction to ammonium (DNRA; e.g., Ignavibacteriaceae), and sulfide-dependent chemolithoautotrophy (e.g., Sulfurovaceae) were enriched and active in less disturbed samples. These findings are supported by insights from nine deeply sequenced metagenomes and 169 derived metagenome-assembled genomes. Altogether, these findings suggest that hydrodynamic disturbance is a critical factor controlling microbial community assembly and biogeochemical processes in coastal sediments. Moreover, they strengthen our understanding of the relationships between microbial composition and biogeochemical processes in these unique environments.Subject terms: Water microbiology, Biogeochemistry