Qingyun Yan

Temperature mediates continental-scale diversity of microbes in forest soils

Climate warming is increasingly leading to marked changes in plant and animal biodiversity, but it remains unclear how temperatures affect microbial biodiversity, particularly in terrestrial soils. Here we show that, in accordance with metabolic theory of ecology, taxonomic and phylogenetic diversity of soil bacteria, fungi and nitrogen fixers are all better predicted by variation in environmental temperature than pH. However, the rates of diversity turnover across the global temperature gradients are substantially lower than those recorded for trees and animals, suggesting that the diversity of plant, animal and soil microbial communities show differential responses to climate change. To the best of our knowledge, this is the first study demonstrating that the diversity of different microbial groups has significantly lower rates of turnover across temperature gradients than other major taxa, which has important implications for assessing the effects of human-caused changes in climate, land use and other factors.

Impacts of the Three Gorges Dam on microbial structure and potential function

The Three Gorges Dam has significantly altered ecological and environmental conditions within the reservoir region, but how these changes affect bacterioplankton structure and function is unknown. Here, three widely accepted metagenomic tools were employed to study the impact of damming on the bacterioplankton community in the Xiangxi River. Our results indicated that bacterioplankton communities were both taxonomically and functionally different between backwater and riverine sites, which represent communities with and without direct dam effects, respectively. There were many more nitrogen cycling Betaproteobacteria (e.g., Limnohabitans), and a higher abundance of functional genes and KEGG orthology (KO) groups involved in nitrogen cycling in the riverine sites, suggesting a higher level of bacterial activity involved in generating more nitrogenous nutrients for the growth of phytoplankton. Additionally, the KO categories involved in carbon and sulfur metabolism, as well as most of the detected functional genes also showed clear backwater and riverine patterns. As expected, these diversity patterns all significantly correlated with environmental characteristics, confirming that the bacterioplankton communities in the Xiangxi River were really affected by environmental changes from the Three Gorges Dam. This study provides a first comparative metagenomic insight for evaluating the impacts of the large dam on microbial function.

Factors influencing the grass carp gut microbiome and its effect on metabolism

Gut microbiota have attracted extensive attention recently because of their important role in host metabolism, immunity and health maintenance. The present study focused on factors affecting the gut microbiome of grass carp (Ctenopharyngodon idella) and further explored the potential effect of the gut microbiome on metabolism. Totally, 43.39 Gb of screened metagenomic sequences obtained from 24 gut samples were fully analysed. We detected 1228 phylotypes (116 Archaea and 1112 Bacteria), most of which belonged to the phyla Firmicutes, Proteobacteria and Fusobacteria. Totally, 41335 of the detected open reading frames (ORFs) were matched to Kyoto Encyclopedia of Genes and Genomes pathways, and carbohydrate and amino acid metabolism was the main matched pathway deduced from the annotated ORFs. Redundancy analysis based on the phylogenetic composition and gene composition of the gut microbiome indicated that gut fullness and feeding (i.e. ryegrass vs. commercial feed, and pond-cultured vs. wild) were significantly related to the gut microbiome. Moreover, many biosynthesis and metabolism pathways of carbohydrates, amino acids and lipids were significantly enhanced by the gut microbiome in ryegrass-fed grass carp. These findings suggest that the metabolic role played by the gut microbiome in grass carp can be affected by feeding. These findings contribute to the field of fish gut microbial ecology and also provide a basis for follow-up functional studies.

Host Species as a Strong Determinant of the Intestinal Microbiota of Fish Larvae

We investigated the influence of host species on intestinal microbiota by comparing the gut bacterial community structure of four cohabitating freshwater fish larvae, silver carp, grass carp, bighead carp, and blunt snout bream, using denaturing gradient gel electrophoresis (DGGE) of the amplified 16S and 18S rRNA genes. Similarity clustering indicated that the intestinal microbiota derived from these four fish species could be divided into four groups based on 16S rRNA gene similarity, whereas the eukaryotic 18S rRNA genes showed no distinct groups. The water sample from the shared environment contained microbiota of an independent group as indicated by both 16S and 18S rRNA genes segments. The bacterial community structures were visualized using rank-abundance plots fitted with linear regression models. Results showed that the intestinal bacterial evenness was significantly different between species (P<0.05) and between species and the water sample (P<0.01). Thirty-five relatively dominant bands in DGGE patterns were sequenced and grouped into five major taxa: Proteobacteria (26), Actinobacteria (5), Bacteroidetes (1), Firmicutes (2), and Cyanobacterial (1). Six eukaryotes were detected by sequencing 18S rRNA genes segments. The present study suggests that the intestines of the four fish larvae, although reared in the same environment, contained distinct bacterial populations, while intestinal eukaryotic microorganisms were almost identical.

Spatiotemporal heterogeneity of plankton communities in Lake Donghu, China, as revealed by PCR-denaturing gradient gel electrophoresis and its relation to biotic and abiotic factors

The 16S and 18S rRNA genes of planktonic organisms derived from five stations with nutrient gradients in Lake Donghu, China, were studied by PCR-denaturing gradient gel electrophoresis (DGGE) fingerprinting, and the relationships between the genetic diversity of the plankton community and biotic/abiotic factors are discussed. The concentrations of total nitrogen (TN), total phosphorus (TP), NH(4)-N and As were found to be significantly related (P<0.05) to morphological composition of the plankton community. Both chemical and morphological analyses suggested that temporal heterogeneity was comparatively higher than spatial heterogeneity in Lake Donghu. Although the morphological composition was not identical to the DGGE fingerprints in characterizing habitat similarity, the two strongest eutrophic stations (I and II) were always initially grouped into one cluster. Canonical correspondence analysis suggested that the factors strongly correlated with the first two ordination axes were seasonally different. The concentrations of TN and TP and the densities of rotifers and crustaceans were generally the main factors related to the DGGE patterns of the plankton communities. The study suggested that genetic diversity as depicted by metagenomic techniques (such as PCR-DGGE fingerprinting) is a promising tool for ecological study of plankton communities and that such techniques are likely to play an increasingly important role in assessing the environmental conditions of aquatic habitats.

Genetic Diversity of Plankton Community as Depicted by PCR-DGGE Fingerprinting and its Relation to Morphological Composition and Environmental Factors in Lake Donghu

To collect information about the genetic diversity of the plankton community and to study how plankton respond to environmental conditions, plankton samples were collected from five stations representing different trophic levels in a shallow, eutrophic lake (Lake Donghu), and investigated by PCR-DGGE fingerprinting. A total of 100 bands (61 of 16S rDNA bands and 39 of 18S rDNA bands) were detected. The DGGE bands unique to any single station accounted for 38% of the total bands, whereas common bands detected at all five stations accounted for only 11%. Using UPGMA clustering and MDS ordination of DGGE fingerprints, stations I and II were found to initially group together into one cluster, which was later joined by station V. Stations III and IV were isolated into two separate groups of one station each. Some differences in grouping relationships were found when analysis was completed on the basis of chemical characteristics and morphological composition, with zooplankton composition showing the greatest variability. However, the most similar stations (I and II) were always initially grouped into one cluster. Moreover, stations that exhibited the same or similar trophic level (stations III and IV), but different concentrations of heavy metals, were further differentiated by the DGGE method. Results of the present study indicated that PCR-DGGE fingerprinting was more sensitive than the traditional methods, as other studies suggested. Additionally, PCR-DGGE appears to be more appropriate for diversity characterization of the plankton community, as it is more canonical, systematic, and effective. Most importantly, fingerprinting results are more convenient for the comparative analyses between different studies. Therefore, the use of the described fingerprinting analysis may provide an operable and sensitive biomonitoring approach to identify critical, and potentially negative, stress within an aquatic ecosystem.

Gut Microbiota Contributes to the Growth of Fast-Growing Transgenic Common Carp (Cyprinus carpio L.)

Gut microbiota has shown tight and coordinated connection with various functions of its host such as metabolism, immunity, energy utilization, and health maintenance. To gain insight into whether gut microbes affect the metabolism of fish, we employed fast-growing transgenic common carp (Cyprinus carpio L.) to study the connections between its large body feature and gut microbes. Metagenome-based fingerprinting and high-throughput sequencing on bacterial 16S rRNA genes indicated that fish gut was dominated by Proteobacteria, Fusobacteria, Bacteroidetes and Firmicutes, which displayed significant differences between transgenic fish and wild-type controls. Analyses to study the association of gut microbes with the fish metabolism discovered three major phyla having significant relationships with the host metabolic factors. Biochemical and histological analyses indicated transgenic fish had increased carbohydrate but decreased lipid metabolisms. Additionally, transgenic fish has a significantly lower Bacteroidetes:Firmicutes ratio than that of wild-type controls, which is similar to mammals between obese and lean individuals. These findings suggest that gut microbiotas are associated with the growth of fast growing transgenic fish, and the relative abundance of Firmicutes over Bacteroidetes could be one of the factors contributing to its fast growth. Since the large body size of transgenic fish displays a proportional body growth, which is unlike obesity in human, the results together with the findings from others also suggest that the link between obesity and gut microbiota is likely more complex than a simple Bacteroidetes:Firmicutes ratio change.

Comparative study on gastrointestinal microbiota of eight fish species with different feeding habits

To reveal the effects of fish genotype, feeding habits and serum physiological index on the composition of gastrointestinal microbiota, eight fish species with four different feeding habits were investigated.

How much metagenomic sequencing is enough to achieve a given goal

Metagenomic studies have dramatically expanded our knowledge of the microbial world. Furthermore, the amount of sample for sequencing has significantly increased with the development of high-throughput sequencing technologies. However, fully capturing all DNA sequences carried by every microorganism in the environment is still impossible. Therefore, estimating a reasonable and practical amount for sequencing to achieve the objectives is particularly necessary. In the present study, we introduce a novel method for estimating the required minimum amount for metagenomic sequencing for a given goal. We also calculated the genomic proportion of each operational taxonomic unit and the detection efficiency of a specific gene (we have used SSU rRNA gene as an example) based on a given amount for random metagenomic sequencing. The reasonable and practical estimated amount for sequencing in metagenomic studies will provide good reference information when applying high-throughput sequencing for a given goal.

Impacts of algal blooms removal by chitosan-modified soils on zooplankton community in Taihu Lake, China

It is important to assess the effect on zooplankton when perform the environmental protection or restoration technology, especially removing algal blooms, because algae were the major primary producer in algal lakes. The influence on zooplankton community after half a year of algal blooms removed by chitosan-modified soils in Taihu Lake was assessed and the rationality of carrying out the process semiannually was evaluated in the present study. Morphological composition and genetic diversity of zooplankton community were investigated by microscope checkup and polymerase chain reaction-denatured gradient gel electrophoresis (PCR-DGGE). A total of 44 zooplankton taxa (23 protozoa, 17 rotifers, 3 copepoda and 1 cladocera) were detected by microscope checkup, and a total of 91 bands (28 bands amplified by primers F1427-GC and R1616, 63 bands amplified by primers Fung-GC and NS1) were detected by PCR-DGGE. The results of cluster analysis or detrended correspondence analysis indicated that there was no considerable difference in morphological composition of zooplankton and DGGE profiles between experimental and control sites, and DGGE profiles could represent the biologic diversity. The study showed that zooplankton community could recover original condition after half year of algal blooms removed by chitosan-modified soils and it was acceptable to apply this process semiannually. In addition, the results revealed that PCR-DGGE could be applied to investigate the impacts of the environmental protection or restoration engineering on zooplankton community diversity.