Metagenomics as a new technological tool to gain scientific knowledge

Metagenomics (also Environmental Genomics, Ecogenomics or Community Genomics) is an emerging approach to studying microbial communities in the environment. This relatively new technique enables studies of organisms that are not easily cultured in a laboratory, thus differing from traditional microbiology that relies almost entirely on cultured organisms. Metagenomics technology thus holds the premise of new depths of understanding of microbes and, importantly, is a new tool for addressing biotechnological problems, without tedious cultivation efforts. DNA sequencing technology has already made a significant breakthrough, and generation of gigabase-pairs of microbial DNA sequences is not posing a challenge any longer. However, conceptual advances in microbial science will not only rely on the availability of innovative sequencing platforms, but also on sequence-independent tools for getting an insight into the functioning of microbial communities. This is an important issue, as we know that even the best annotations of genomes and metagenomes only create hypotheses of the functionality and substrate spectra of encoded proteins which require experimental testing by classical disciplines such as physiology and biochemistry. In this review, we address the following question, how to take advantage of, and how can we improve the, metagenomic technology for accommodating the needs of microbial biologists and enzymologists?     

高矿浆浓度下黄铜矿浸出过程中微生物群落结构变化规律

目的：为阐明微生物群落演替及功能与浸出效率之间关系奠定基础,以及如何提高黄铜矿生物浸出效率和铜回收率提供理 论依据。方法：通过连续传代培养进行驯化,使得复合菌群的矿浆浓度耐受能力达到25 %（w/v）。采用该复合菌群在25 %矿浆浓 度下浸出黄铜矿,同时利用变性梯度凝胶电泳和克隆文库技术分析浸出过程中的微生物多样性。最后,采用实时荧光定量PCR 对 浸出过程中微生物群落结构进行定量解析。结果：28天内黄铜矿浸出率能够达到95.1 %,而驯化前的浸出率只有51.5%。该复合 菌群主要由Acidithiobacillus caldus, Sulfobacillus acidophilus,和Fereoplasma theroplasma thermophilum组成,其中Acidithbacillus caldus是浸出前期和后期的优势种群,而Sulfobacillus acidophilus在浸出中期均有竞争优势, Ferroplasma thermophilum在整个浸出过程中占 据整个群落的比例均较低。结论：本研究获得的复合菌群具有较强的浸出黄铜矿能力, Acidithiobacillus caldus和Sulfobacillus acidophilus在浸出过程中起着重要的作用,pH 值和铜浸出率与群落结构相关性较高。     

肠道微生物菌群分型的研究进展

人体肠道内存在着处于动态平衡中的复杂微生物群体,包含1000多种细菌和古生菌等共生微生物。它们广泛参与人体的营养、代谢和免疫等生理过程,是影响健康最重要的因素之一。同一个体不同胃肠道部位的微生物群落组成显著不同,而在不同个体的肠道微生物群落组成也存在很大差异。肠道微生物群落结构受到饮食习惯、药物干预以及生活环境等因素影响,形成了不同个体间菌群组成的差异。通过菌群测序分析和群体分型,可以将不同个体的肠道微生物群落组成分为拟杆菌、普氏菌和瘤胃球菌三种肠型。确定肠道微生物群落结构的分型,将复杂的肠道微生物系统模式化,有利于对大样本肠道微生物菌群进行分析,更好地指导相关疾病的诊断和治疗。本文综述了肠道微生物的分型和相关影响因素的进展。     

上海市崇明区猪—土壤界面微生态与抗生素耐药性相关性分析

探究养殖场内育肥猪粪便与土壤的微生物组成和抗生素耐药基因构成,并挖掘之间的关联。

选择上海市崇明区5家猪养殖场,采集猪粪便和土壤样本,使用Illumina NovaSeq 6000高通量测序平台进行全基因组鸟枪法测序。通过主坐标分析、LEfSe分析、共现网络分析和统计学检验,探究样本微生物组成、多样性特征和抗生素耐药基因之间的关系。

猪粪便中的主要微生物包括拟杆菌门、厚壁菌门、变形菌门和放线菌门,主要耐药基因类型包括多药耐药类、四环素类、糖肽类、肽类、氟喹诺酮类和β-内酰胺类等。来自同一养猪场的样本在微生物丰度和耐药基因多样性上存在相关性。此外,研究还发现养猪场运作因素如饲料成分、饲养密度和卫生环境等,导致了不同养猪场之间的微生物组成和耐药基因的差异。在猪粪—土壤界面,一些有益微生物之间存在共生关系,具有抑制潜在病原微生物的生长能力,并对土壤微生态产生影响。不同类型的耐药基因之间也存在共生关系。

通过宏基因组学方法研究了猪粪便与土壤中的微生物和耐药基因,揭示了微生物与抗生素耐药基因之间的相关性,提出微生物群是耐药基因谱的重要驱动因素。这一发现为通过微生态调控来预防和控制抗生素耐药性提供了科学依据。

     

Current status and prospects on microbial control in Japan

Historically in Japan, studies on the diseases of the silkworm, Bombyx mori, as a factor affecting the well-being of the silk industry, have dominated insect pathology. However, work by Hidaka in 1933 demonstrated the possibility of controlling the pine moth, Dendrolimus spectabilis, with the fungus Beauveria bassiana and since then, various attempts have been made to develop a method to control insect pests using insect pathogens. The cypovirus product, Matsukemin, was the first microbial control product to be registered in 1974, and inactive and live Bacillus thuringiensis products were also registered and put on the market as pesticides in 1981 and 1982, respectively. Currently, there are 25 microbial insecticides on the market that constitute slightly less than 2% of all insecticides used in Japan. Adoption of biopesticides is likely to increase in the near future due to scientific advances and several new government policies that encourage the use of alternative pest control products.     

云南哀牢山退化常绿阔叶林乔木多样性和生物量的恢复

为了探究退化森林的树种组成变化和生物量储量的恢复规律,该研究选取云南哀牢山不同演替阶段的常绿阔叶林为对象,比较了不同演替阶段森林群落结构、树种多样性和生物量变化。结果表明,从演替早期到演替末期,乔木的科数先减少后增多,属数和种数则逐渐增加;Margalef丰富度指数、Simpson优势度指数、Shannon-Wiener多样性指数和Pielou均匀度指数随演替进程均呈增加的趋势;乔木生物量储量随演替进程逐渐升高,演替早期和演替中期的生物量分别为演替末期生物量的9.87%和65.98%;群落水平的树种多样性指数与总生物量呈显著正相关关系(P<0.05)。树木的生长和树种多样性的提高是影响群落乔木生物量储量递增的因素,且哀牢山处于湿冷的气候条件,退化森林植被的恢复相对比较缓慢。     

Polyphasic Taxonomy of Novel Actinobacteria Showing Macromolecule Degradation Potentials in Bigeum Island,Korea

Aerobic, alkaliphilic to alkalitolerant and mesophilic bacteria were isolated and characterized from soil and sediment samples collected from Bigeum Island, South Korea. The total numbers of microorganisms in the soil and sediment samples were found to be 10³–10⁵ cfu/g and 10²–10⁷ cfu/g, respectively. A total of 163 isolates were isolated and subjected to further characterization on the basis of pH, temperature and salt tolerance. Among the 163 isolates, 54 were selected based on their tolerance attributes to temperature, pH and NaCl. Out of the 54 isolates, 27 were further selected based on their multiple tolerance ability and enzyme profile and were subjected to 16S rRNA gene sequencing and phylogenetic analysis. The latter indicated that most of the Bigeum Island isolates were related to the phylum Actinobacteria. The phylogenetic tree based on 16S rRNA gene sequences placed the 27 isolates into 9 different major bacterial genera, each genus comprising pure cultures that shared ≤97% sequence identity and 18 putative novel species. Most of the strains were alkalitolerant and mesophilic, and produced biotechnologically important enzymes at alkaline pH.     

Human microbiomics

The sequencing of the human genome has driven the study of human biology in a significant way and enabled the genome-wide study to elucidate the molecular basis of complex human diseases. Recently, the role of microbiota on human physiology and health has received much attention. The influence of gut microbiome (the collective genomes of the gut microbiota) in obesity has been demonstrated, which may pave the way for new prophylactic and therapeutic strategies such as bacteriotherapy. The significance and recent understandings in the area of “human microbiomics” are discussed here.     

宏蛋白质组学——研究微生物群落基因表达的新技术

宏蛋白质组学是应用蛋白质组学技术对微生物群落进行研究的一项新技术,其定义为在特定的时间对微生物群落的所有蛋白质组成进行大规模鉴定。通过对宏蛋白质组学的研究策略、进展情况的综述、介绍,展望了宏蛋白组学在研究微生物群落基因表达中的应用前景。     

Effects of grazing disturbance on plant diversity,community structure and direction of succession in an alpine meadow on Tibet Plateau,China

To elucidate the effects of grazing intensity and grazing time on plant diversity and community structure, as well as the successional differentiation in an alpine meadow, a controlled grazing trial, with six grazing intensities on an alpine meadow was conducted in the eastern Qilian Mountain region for four years. Using species accumulation curves, RDA ordination and variance decomposition, we analyzed the changes in proportion of dominant species, richness, abundance, as well as the life forms of plant communities under grazing disturbance. Both the grazing intensity and grazing time had a significant effect on these dominant species, richness, abundance, as well as the life forms in the plant community (P < 0.01). More detailed results showed that: (1) The richness and abundance of plant species were highest in the light grazing plot, and these increased as time passed. In the heavy grazing plot, the abundance of plant species decreased as time passed, but the richness of these species did not change significantly. (2) The abundance of Gramineae and Umbelliferae were negatively and significantly correlated with the duration of grazing treatments, whereas Plantaginaceae and Geraniaceae were positively and significantly correlated with the grazing intensity. Over time, the abundance of bunch-type plants decreased and other life forms of plants have increased. With the increase in grazing intensity, the plants' abundance with the rosette type did not change, but other life forms of plants decreased. The results of variance decomposition indicated that grazing disturbance has had greater effects on life forms and plant populations, followed by the changes in the dominant species and their abundance, with lesser effects on the richness of the species. Grazing intensity had a greater effect than the duration of the grazing treatment had. The results of PCA showed that the climax community in both the lowest and the highest grazing intensity plots had changed over time. In the sample plots with light grazing intensity, the plant community changed to an Elymus nutans + Poa crymophila community, but later changed to a Melilotoides ruthenicus + Kobresia humilis community under heavy grazing.     

Effects of grazing disturbance on plant diversity,community structure and direction of succession in an alpine meadow on Tibet Plateau,China

To elucidate the effects of grazing intensity and grazing time on plant diversity and community structure, as well as the successional differentiation in an alpine meadow, a controlled grazing trial, with six grazing intensities on an alpine meadow was conducted in the eastern Qilian Mountain region for four years. Using species accumulation curves, RDA ordination and variance decomposition, we analyzed the changes in proportion of dominant species, richness, abundance, as well as the life forms of plant communities under grazing disturbance. Both the grazing intensity and grazing time had a significant effect on these dominant species, richness, abundance, as well as the life forms in the plant community (P < 0.01). More detailed results showed that: (1) The richness and abundance of plant species were highest in the light grazing plot, and these increased as time passed. In the heavy grazing plot, the abundance of plant species decreased as time passed, but the richness of these species did not change significantly. (2) The abundance of Gramineae and Umbelliferae were negatively and significantly correlated with the duration of grazing treatments, whereas Plantaginaceae and Geraniaceae were positively and significantly correlated with the grazing intensity. Over time, the abundance of bunch-type plants decreased and other life forms of plants have increased. With the increase in grazing intensity, the plants' abundance with the rosette type did not change, but other life forms of plants decreased. The results of variance decomposition indicated that grazing disturbance has had greater effects on life forms and plant populations, followed by the changes in the dominant species and their abundance, with lesser effects on the richness of the species. Grazing intensity had a greater effect than the duration of the grazing treatment had. The results of PCA showed that the climax community in both the lowest and the highest grazing intensity plots had changed over time. In the sample plots with light grazing intensity, the plant community changed to an Elymus nutans + Poa crymophila community, but later changed to a Melilotoides ruthenicus + Kobresia humilis community under heavy grazing.     

Bacterial abundance and diversity in the Barbados Trench determined by phospholipid analysis

Abstract: The Barbados trench is characterized by large fields of volcanoes and mounds located over a distance of 30 km above the northern slope of a basement ridge corresponding to an inactive transform fault. Sediments from various locations were collected and analyzed for their lipid contents. Bacterial input to the overall biomass was estimated through the analysis of phospholipid ester-linked fatty acid (PLFA) profiles and glycerol ether lipids. Results indicated a eubacterial biomass estimated to be 10⁹cells (g dry wt)⁻¹. Individual fatty acid profiles revealed the presence of sulfur-oxidizing bacteria common to many deep-sea sites but also a large contribution of type I and type II methanotrophs to the eubacterial biomass. The presence of methanotrophs was further supported by the analysis of specific biomarkers of these microorganisms as well as some unusual trans fatty acid isomers. Anaerobic bacteria and presumbly sulfate reducing bacteria were also present, as well as archaebacteria and primarily methanogens, as indicated by glycerol ether lipid analysis.     

免培养法对一热泉细菌多样性的初步研究

应用免培养法（Cultureindependent）对云南腾冲热海大滚锅高温热泉中细菌的多样性进行初步的分析。经过克隆筛选,测定了5个克隆的16S rDNA插入片段的近全序列,系统发育分析的结果表明,它们分属于Bacillus、Hydrogenobacter和Pseudomonas,有一个克隆尚难确定其分类地位,它属于Thermodesulfobacteriaceae科,介于Geothermbacterium属和Thermodesulfobacteria属之间。经PCR扩增出上述5个克隆16S rDNA插入序列中及环境样品总DNA中的16S rDNA V8高变区约600bp片段,进行变性梯度电泳（DGGE）。所得电泳图谱和5个序列的系统发育树不仅表明该高温热泉存在着丰富的细菌多样性,还显示了它们是该高温热泉中细菌的优势物种。     

青藏高原东部采伐迹地早期人工重建序列梯度上植物多样性的变化

 采伐是青藏高原东部亚高山森林过去经营管理中最常见的实践。采伐的一个重要后果就是林地生物多样性的衰退和损失。目前虽然对采伐环境退化与迹地人工林恢复重建开展过许多研究,但对采伐迹地以及人工重建过程中的生物多样性变化研究很少。人工重建时间序列上的植物组成变化还不清楚,也没有人去检测人工林早期发展阶段间多样性的差异。作者选择大渡河上游亚高山针叶林序列采伐迹地,调查了采伐后8个人工造林时间序列梯度（1年、2年、5年、7年、10年、15年、19年和30年）和相邻的原始林内的物种组成和丰富度,比较分析了序列梯度上的植物     

Impact of long-term conventional and organic farming on the diversity of arbuscular mycorrhizal fungi

Previous work has shown considerably enhanced soil fertility in agroecosystems managed by organic farming as compared to conventional farming. Arbuscular mycorrhizal fungi (AMF) play a crucial role in nutrient acquisition and soil fertility. The objective of this study was to investigate the diversity of AMF in the context of a long-term study in which replicated field plots, at a single site in Central Europe, had been cultivated for 22 years according to two organic and two conventional farming systems. In the 23rd year, the field plots, carrying an 18-month-old grass-clover stand, were examined in two ways with respect to AMF diversity. Firstly, AMF spores were isolated and morphologically identified from soil samples. The study revealed that the AMF spore abundance and species diversity was significantly higher in the organic than in the conventional systems. Furthermore, the AMF community differed in the conventional and organic systems: Glomus species were similarly abundant in all systems but spores of Acaulospora and Scutellospora species were more abundant in the organic systems. Secondly, the soils were used to establish AMF-trap cultures using a consortium of Plantago lanceolata, Trifolium pratense and Lolium perenne as host plants. The AMF spore community developing in the trap cultures differed: after 12 months, two species of the Acaulosporaceae (A. paulinae and A. longula) were consistently found to account for a large part of the spore community in the trap cultures from the organic systems but were found rarely in the ones from the conventional systems. The findings show that some AMF species present in natural ecosystems are maintained under organic farming but severely depressed under conventional farming, indicating a potentially severe loss of ecosystem function under conventional farming.     

Sequencing our way to more accurate community abundance

Over the last two decades, there has been a huge increase in our understanding of microbial diversity, structure and composition enabled by high-throughput sequencing technologies. Yet, it is unclear how the number of sequences translates to the number of cells or species within the community. In some cases, additional observational data may be required to ensure relative abundance patterns from sequence reads are biologically meaningful. The goal of DNA-based methods for biodiversity assessments is to obtain robust community abundance data, simultaneously, from environmental samples. In this issue of Molecular Ecology Resources, Pierella Karlusich et al. (2022) describe a new method for quantifying phytoplankton cell abundance. Using Tara Oceans data sets, the authors propose the photosynthetic gene psbO for reporting accurate relative abundance of the entire phytoplankton community from metagenomic data. The authors demonstrate higher correlations with traditional optical methods (including microscopy and flow cytometry), using their new method, improving upon molecular abundance assessments using multicopy marker genes. Furthermore, to facilitate application of their approach, the authors curated a psbO gene database for accessible taxonomic queries. This is an important step towards improving species abundance estimates from molecular data and eventually reporting of absolute species abundance, enhancing our understanding of community dynamics.     

Strategies for accessing soil metagenome for desired applications

Most of the microorganisms in nature are inaccessible as they are uncultivable in the laboratory. Metagenomic approaches promise the accessibility of the genetic resources and their potential applications. Genetic resources from terrestrial environments can be accessed by exploring the soil metagenome. Soil metagenomic analyses are usually initiated by the isolation of environmental DNAs. Several methods have been described for the direct isolation of environmental DNAs from soil and sediments. Application of metagenomics largely depends on the construction of genomic DNA libraries and subsequent high-throughput sequencing or library screening. Thus, obtaining large quantities of pure cloneable DNA from the environment is a prerequisite. This review discusses the recent developments related to efficient extraction and purification of soil metagenome highlighting the considerations for various metagenomic applications.     

活性污泥微生物群落宏组学研究进展

活性污泥是全球最常用的废水生物处理人工生态系统,微生物是驱动其污染净化能力的关键。活性污泥微生物群落所有物种与基因(简称\"微生物组\")的研究先后经历了\"显微镜观察和纯菌培养分离\"(1915)、\"PCR扩增-测序\"(1994)和\"高通量测序-宏组学分析\"(2006)三个重要阶段的发展变迁。相应地,我们对活性污泥微生物组的认知经历了从最早对微型动物(如钟虫和轮虫)及其他微生物的形貌观察和纯种培养鉴定到今天对整个微生物组的全局多样性认识的飞跃。近13年来,基于高通量测序的宏组学方法被广泛应用于揭示活性污泥微生物群落组成结构和功能,我们现在充分意识到活性污泥微生物组蕴藏着大量不可培养新物种和基因多样性,驱动着各类污染物的降解与转化。目前,特异性分子标记基因的扩增子测序技术已经被广泛应用于揭示城市和工业废水处理活性污泥微生物组和典型功能种群(如硝化细菌和聚磷菌)的时空多样性和群落构建机制,进而为未来实现活性污泥微生物组功能的精准调控奠定理论基础。宏基因组学研究在群落、种群和个体基因组水平全面解析了活性污泥微生物组驱动的碳、氮、磷元素循环过程,以及有机微污染物的生物降解和转化机理。将来活性污泥微生物组学研究需要在\"标准化的组学分析方法和绝对定量\"\"高通量培养组学\"\"高通量功能基因组学\"和\"多组学方法的结合及多种方法并用\"4个方面取得实现精准生态基因组学所需的技术突破,以最大限度发掘活性污泥微生物组在污水处理与资源回收领域的生态学与工程学价值。     

Relationship between species relative abundance and plant traits for an infertile habitat

This study tested whether differences in species abundance at an infertile site could be explained by differences in the species' plant traits. Nine traits were chosen for the analysis based on results of previous studies conducted across soil fertility gradients. The traits were measured for each of seven herbaceous species whose abundance ranged from 5% to 100% of locations occupied in a ridgetop habitat. Using linear regression, significant relationships were found between species relative abundance and each of five traits. In these relationships, a trait explained between 69% and 88% of interspecific variation in abundance. Relatively abundant species had a slower growth rate, smaller shoot mass, higher root to shoot ratio, slower loss of leaf tissue to herbivores and higher infection of roots by mycorrhizal fungi than less abundant species. Using three of these five traits (i.e. shoot mass, mycorrhizal infection and loss of leaf tissue to herbivores) as independent variables in a multiple regression equation explained 99% of interspecific variation in abundance. The latter result indicates that species relative abundance can be explained for a single habitat by choosing traits found to be related to species abundance in previous gradient studies. However, not every trait chosen was significantly related to species abundance. Therefore, a large number of traits may have to be chosen initially to ensure that some subset of these traits can explain species relative abundance.