Biogeography of the ecosystems of the healthy human body

Background

Characterizing the biogeography of the microbiome of healthy humans is essential for understanding microbial associated diseases. Previous studies mainly focused on a single body habitat from a limited set of subjects. Here, we analyzed one of the largest microbiome datasets to date and generated a biogeographical map that annotates the biodiversity, spatial relationships, and temporal stability of 22 habitats from 279 healthy humans.

Results

We identified 929 genera from more than 24 million 16S rRNA gene sequences of 22 habitats, and we provide a baseline of inter-subject variation for healthy adults. The oral habitat has the most stable microbiota with the highest alpha diversity, while the skin and vaginal microbiota are less stable and show lower alpha diversity. The level of biodiversity in one habitat is independent of the biodiversity of other habitats in the same individual. The abundances of a given genus at a body site in which it dominates do not correlate with the abundances at body sites where it is not dominant. Additionally, we observed the human microbiota exhibit both cosmopolitan and endemic features. Finally, comparing datasets of different projects revealed a project-based clustering pattern, emphasizing the significance of standardization of metagenomic studies.

Conclusions

The data presented here extend the definition of the human microbiome by providing a more complete and accurate picture of human microbiome biogeography, addressing questions best answered by a large dataset of subjects and body sites that are deeply sampled by sequencing.     

Efficient rescue of threatened biodiversity data using reBiND workflows

Abstract

Biodiversity data generated in the context of research projects often lack a strategy for long-term preservation and availability, and are therefore at risk of becoming outdated and finally lost. The reBiND project aims to develop an efficient and well-documented workflow for rescuing such data sets. The workflow consists of phases for data transformation into contemporary standards, data validation, storage in a native XML database, and data publishing in international biodiversity networks. It has been developed and tested using the example of collection and observational data but is flexible enough to be transferred to other data types and domains.     

Forest ecosystem inventory and monitoring as a framework for terrestrial natural renewable resource survey programmes

ABSTRACT

The established practice of forest ecosystem inventory and monitoring is recognised as a main support for terrestrial natural renewable resource survey programmes. Inventory and monitoring programmes focused on an overall assessment of ecosystem attributes evolving into global environmental survey programmes have been devised, but implementation is still quite contradictory. The state-of-the-art is discussed here, with special reference to the European Union and Italy. Topical issues are reviewed, with selective concern to: remote sensing capability, probability sampling, forest type (habitat) classification and landscape ecology, sustainable management indicators. Benefits brought by information technology are highlighted. Its development and the implementation of approaches based on a sound “per habitat” landscape ecological perspective will bring unique benefits, thus leading to an effective integration among sector surveys aimed at global environmental inventory/monitoring.     

Testing indicators of biodiversity for plantation forests

In many parts of the world, plantations make up a considerable proportion of the total forest area. In such regions, the identification of high biodiversity value stands and of management practices to enhance biodiversity is essential if the goals of Sustainable Forest Management are to be achieved. Since complete biodiversity assessments are rarely possible, efforts have been increasingly focussed on the use of indicators. Of particular interest are indicators applicable to individual stands that require no specialist taxonomic or technical knowledge to assess. Candidate biodiversity indicators had been identified in a previous study using data from Irish Sitka spruce (Picea sitchensis) and ash (Fraxinus excelsior) plantations but had yet to be tested on independent data. In the present study, the provisional indicators for vascular plant, bryophyte, spider and bird diversity were tested on data from Irish Scots pine (Pinus sylvestris), oak (Quercus petraea/Quercus robur), Sitka spruce and lodgepole pine (Pinus contorta) plantations. Conifer canopy cover was confirmed as an important biodiversity indicator, due to its influence on below-canopy microclimatic and structural conditions. Bryophyte species richness was higher in relatively high canopy cover plantations on poorly drained soils, while bird species richness was higher in more open plantations with high shrub cover. Coarse woody debris was an important substrate for forest-associated bryophytes, with higher species richness at higher volumes of deadwood. Both proximity to old woodland and stand age were confirmed as positive indicators for forest-associated vascular plants. This is related to dispersal limitation in these species, with nearby woodlands acting as important seed sources and colonisation increasing with time. Stand age was also confirmed as a positive indicator for forest-associated spiders and is related to the development of suitable habitat as the plantation matures. All of the confirmed indicators can be assessed without need for specialist knowledge, are ecologically meaningful and applicable to a range of forests managed under a clearfelling system. They can be used to assess the potential value of stands for the taxonomic groups to which they apply, as well as giving insights into management practices to enhance diversity in these groups.     

利用红外相机调查祁连山国家公园(青海片区)兽类和鸟类多样性

2017年5-9月,采用红外相机调查祁连山国家公园(青海片区)兽类和鸟类多样性。共布设154个相机位点,累计12 096个相机日,共获得9 675张有效独立照片,鉴定23种野生兽类和50种野生鸟类物种,分别隶属5目10科和9目19科,另记录到家畜5种。相对多度指数最高的前五种野生动物依次为岩羊(Pseudois rnayaur)(18.23)、喜马拉雅旱獭(Marmota himalayarea)(15.98)、灰尾兔(Lepus oiostolus)(5.06)、红嘴山鸦(Pyrrhocorax pyrrhocorax)(3.39)、高原鼠兔(Ochotona curzoniae)(2.49)。中国特有物种有荒漠猫(Felis bieti)、白唇鹿(Ceryus albirostris)、西藏马鹿(Cervus wallichii)、藏原羚(Procapra picticaudata)、红耳鼠兔(Ochotana erythrotis)、蓝马鸡(Crossoptilon auritum)和地山雀(Pseudopocdoces humilis)7种。国家Ⅰ级重点保护野生动物有4种,国家Ⅱ级重点保护野生动物有20种;被中国脊椎动物红色名录评估为极危、濒危、易危、近危的物种分别有1种、6种、3种、14种。红外相机调查结果反映出祁连山国家公园(青海片区)兽类和鸟类现状,为祁连山国家公园体制试点生物多样性保护和管理提供基础数据。     

基于红外相机的四川亚丁国家级自然保护区鸟兽多样性初报

2017年5～11月,我们在四川亚丁国家级自然保护区内共布设64台红外相机,对保护区内的兽类和鸟类多样性进行了调查。经过8 394个相机工作日的调查,我们共鉴定出分属9目26科共56种的野生兽类和鸟类,其中国家Ⅰ级、Ⅱ级重点保护野生动物分别有5种和13种,被IUCN红色名录评估为濒危(EN)、易危(VU)、近危(NT)的野生动物分别有2种、3种和6种。相对多度指数居前三位的兽类和鸟类分别是毛冠鹿(Elaphodus cephalophus)、珀氏长吻松鼠(Dremomys pernyi)、猕猴(Macaca mulatta)和血雉(Ithaginis cruentus)、大噪鹛(Garrulax maximus)、雉鹑(Tetraophasis obscurus)。本次调查初步了解了亚丁保护区内鸟兽的种类、丰富度、分布以及人为干扰情况,是亚丁国家级自然保护区第一次开展鸟兽的本底资源调查和研究。我们的调查结果对掌握亚丁国家级自然保护区的鸟兽种类和分布现状等本底资料具有重要意义,同时也为保护区今后的科研工作及开展野生动物的保护管理和长期监测提供了数据支持和指导。     

Rediscovery and phylogenetic placement of Olpidiopsis gillii (de Wildeman) Friedmann,a holocarpic oomycete parasitoid of freshwater diatoms

The genus Olpidiopsis of the Oomycota includes several species that are aquatic parasites and hyperparasites. Despite their widespread occurrence and potential ecological importance, only a handful of these species has been subjected to phylogenetic investigations, so far. Most species have not been observed and reported for several decades. In the current study, the freshwater diatom parasite Olpidiopsis gillii (de Wild.) Friedmann was rediscovered from the river Main in Germany and investigated for its phylogenetic placement using nuclear small ribosomal subunit (SSU) sequences. The absence of a zoospore diplanetism is a characteristic of the genus Olpidiopsis, which is in contrast to the diplanetism observed in species of Ectrogella. The phylogenetic reconstruction revealed that Olpidiopsis gillii is a basal lineage within the oomycetes, grouping together with the recently-described marine diatom parasite Olpidiopsis drebesii with high support, and loosely associated with Olpidiopsis species parasitising red algae. However, as there are no sequence data available for the type species of both Olpidiopsis and Ectrogella the taxonomic assignment of these simple holocarpic parasites of algae and diatoms remains fraught with uncertainty.     

A Study on actinobacterial diversity of Hampoeil cave and screening of their biological activities

Caves are oligotrophic, dark and less-explored environments and are considered as sources of promising microbial strains in biotechnology. Hampoeil Cave is located in massive dolomite with thin bedded limestone in northwestern of Iran. In an isolation and screening program, various samples from soil, water, floor, wall and ceiling of Hampoeil cave and its invertebrates were collected. Four various treatments and 10 different isolation media were used for the isolation of the actinobacteria. Screening of the isolates for antimicrobial activity against 10 bacteria and fungi, 5 hydrolytic enzymes production and resistance to 5 heavy metals have been performed. Among 33 various samples, 76 actinobacteria from various genera, including Streptomyces, Micromonospora, Micrococcus, Kocuria and Corynebacterium were isolated. Eighty percent of the strains had one of the studied hydrolytic enzyme activity. At least one type of antimicrobial activity was seen in 25.3% of the isolates. Resistance to one metal or more was seen in 26.32% of the isolates. The ratio of rare-actinobacteria in the oligotrophic samples to enriched samples is 20% more than Streptomyces. Percentage of strains with the highest activity in esterase, amylase, DNase, protease or lipase activity that were isolated from organic-rich environmental samples were 100, 100, 100, 82 and 82%, respectively. Also, 26.32% of the actinobacterial isolates resisted to heavy metals. It was concluded that Hampoeil cave is a good source in finding cave-living actinobacteria potent in producing hydrolytic enzymes and bioremediation.