Environmental Controls on Microbial Abundance and Activity on the Greenland Ice Sheet: A Multivariate Analysis Approach

Microbes in supraglacial ecosystems have been proposed to be significant contributors to regional and possibly global carbon cycling, and quantifying the biogeochemical cycling of carbon in glacial ecosystems is of great significance for global carbon flow estimations. Here we present data on microbial abundance and productivity, collected along a transect across the ablation zone of the Greenland ice sheet (GrIS) in summer 2010. We analyse the relationships between the physical, chemical and biological variables using multivariate statistical analysis. Concentrations of debris-bound nutrients increased with distance from the ice sheet margin, as did both cell numbers and activity rates before reaching a peak (photosynthesis) or a plateau (respiration, abundance) between 10 and 20 km from the margin. The results of productivity measurements suggest an overall net autotrophy on the GrIS and support the proposed role of ice sheet ecosystems in carbon cycling as regional sinks of CO₂ and places of production of organic matter that can be a potential source of nutrients for downstream ecosystems. Principal component analysis based on chemical and biological data revealed three clusters of sites, corresponding to three ‘glacier ecological zones’, confirmed by a redundancy analysis (RDA) using physical data as predictors. RDA using data from the largest ‘bare ice zone’ showed that glacier surface slope, a proxy for melt water flow, accounted for most of the variation in the data. Variation in the chemical data was fully explainable by the determined physical variables. Abundance of phototrophic microbes and their proportion in the community were identified as significant controls of the carbon cycling-related microbial processes.     

Landscape Controls on Nutrient Stoichiometry Regulate Lake Primary Production at the Margin of the Greenland Ice Sheet

Ecosystems - Global change is reshaping the physical environment and altering nutrient dynamics across the Arctic. These changes can affect the structure and function of biological communities and...     

Phylogenetic and Physiological Diversity of Microorganisms Isolated from a Deep Greenland Glacier Ice Core

We studied a sample from the GISP 2 (Greenland Ice Sheet Project) ice core to determine the diversity and survival of microorganisms trapped in the ice at least 120,000 years ago. Previously, we examined the phylogenetic relationships among 16S ribosomal DNA (rDNA) sequences in a clone library obtained by PCR amplification from genomic DNA extracted from anaerobic enrichments. Here we report the isolation of nearly 800 aerobic organisms that were grouped by morphology and amplified rDNA restriction analysis patterns to select isolates for further study. The phylogenetic analyses of 56 representative rDNA sequences showed that the isolates belonged to four major phylogenetic groups: the high-G+C gram-positives, low-G+C gram-positives, Proteobacteria, and the Cytophaga-Flavobacterium-Bacteroides group. The most abundant and diverse isolates were within the high-G+C gram-positive cluster that had not been represented in the clone library. The Jukes-Cantor evolutionary distance matrix results suggested that at least 7 isolates represent new species within characterized genera and that 49 are different strains of known species. The isolates were further categorized based on the isolation conditions, temperature range for growth, enzyme activity, antibiotic resistance, presence of plasmids, and strain-specific genomic variations. A significant observation with implications for the development of novel and more effective cultivation methods was that preliminary incubation in anaerobic and aerobic liquid prior to plating on agar media greatly increased the recovery of CFU from the ice core sample.     

Diversity and biotechnological potential of microorganisms associated with marine sponges

Marine sponges harbor diverse microbial communities, encompassing not only three domains of life including Bacteria, Archaea and eukaryotes, but also many different phyla within Bacteria. This diversity implies a rich source for biodiscovery of new natural products. Here, we review recent progress in our understanding of this genetic diversity, its retrieval via culture and genomic approaches, and its implications for chemical diversity and other biotechnology applications of sponge microorganisms and their genes.     

Dissolved gases in frozen basal water from the NGRIP borehole: implications for biogeochemical processes beneath the Greenland Ice Sheet

Little information exists on biogeochemical transformations in aquatic ecosystems beneath polar ice sheets (i.e., water-saturated sediments, streams, rivers, and lakes) and their role in global elemental cycles. Subglacial environments may represent important sources of atmospheric CO₂ and/or CH₄ during deglaciation, thus acting as amplifiers in the climate system. However, the role of subglacial environments in global climate processes has been difficult to assess given the absence of biogeochemical data from the basal zones of inland polar ice sheets. Here, we report on the concentrations of CO₂, CH₄, and H₂ in samples of refrozen basal water recovered at a depth of ~3,042 meters below the surface during the North Greenland Ice Core Project (NGRIP). CH₄ and H₂ concentrations in the NGRIP samples were approximately 60- and 700-fold higher, respectively, relative to air-equilibrated water, whereas CO₂ was ~fivefold lower. Metabolic pathways such as (1) methanogenesis, (2) organic matter fermentation, carboxydotrophic, and/or methylotrophic activity, and (3) CO₂ fixation provide plausible biotic explanations for the observed CH₄, H_2, and CO₂ concentrations, respectively.     

根结线虫放线菌及其生物防治活性研究

从感染植物根部的根结线虫卵和雌虫中,分离得到放线菌20株。形态、细胞壁氨基酸组分和16S rRNA基因序列分析表明:分离菌株分属于链霉菌属(Streptomyces)、诺卡氏菌属(Nocardia)和假诺卡氏菌属(Pseudonocardia),其中链霉菌占80.0%。分离菌株对根结线虫Meloidogynespp.卵的平均寄生率、卵的孵化率、幼虫死亡率分别为54.1%、40.4%和26.2%。根据体外测试的结果,选择具有高致病力的3株链霉菌(1-17,2-6,9-47)和1株诺卡氏菌(5-1)进行温室番茄防效测试,其生防效率分别为31.4%、37.7%、56.4%和42.4%。     

Diversity of the human gastrointestinal tract microbiota revisited

Since the early days of microbiology, more than a century ago, representatives of over 400 different microbial species have been isolated and fully characterized from human gastrointestinal samples. However, during the past decade molecular ecological studies based on ribosomal RNA (rRNA) sequences have revealed that cultivation has been able only to access a small fraction of the microbial diversity within the gastrointestinal tract. The increasing number of deposited rRNA sequences calls for the setting up a curated database that allows handling of the excessive degree of redundancy that threatens the usability of public databases. The integration of data from cultivation-based studies and molecular inventories of small subunit (SSU) rRNA diversity, presented here for the first time, provides a systematic framework of the microbial diversity in the human gastrointestinal tract of more than 1000 different species-level phylogenetic types (phylotypes). Such knowledge is essential for the design of high-throughput approaches such as phylogenetic DNA microarrays for the comprehensive analysis of gastrointestinal tract microbiota at multiple levels of taxonomic resolution. Development of such approaches is likely to be pivotal to generating novel insights in microbiota functionality in health and disease.     

Diversity of gut microbiota increases with aging and starvation in the desert locust

Here we report the effects of starvation and insect age on the diversity of gut microbiota of adult desert locusts, Schistocerca gregaria, using denaturing gradient gel electrophoretic (DGGE) analysis of bacterial 16S rRNA genes. Sequencing of excised DGGE bands revealed the presence of only one potentially novel uncultured member of the Gammaproteobacteria in the guts of fed, starved, young or old locusts. Most of the 16S rRNA gene sequences were closely related to known cultured bacterial species. DGGE profiles suggested that bacterial diversity increased with insect age and did not provide evidence for a characteristic locust gut bacterial community. Starved insects are often more prone to disease, probably because they compromise on immune defence. However, the increased diversity of Gammaproteobacteria in starved locusts shown here may improve defence against enteric threats because of the role of gut bacteria in colonization resistance.     

Diversity and antagonistic potential of bacteria associated with bryophytes from nutrient-poor habitats of the Baltic Sea Coast

Very little is known about the interaction of bryophytes with bacteria. Therefore, we analyzed bacteria associated with three bryophyte species, Tortula ruralis, Aulacomnium palustre, and Sphagnum rubellum, which represent typical moss species of three nutrient-poor plant communities at the southern Baltic Sea coast in Germany. By use of two cultivation-independent techniques, denaturing gradient gel electrophoresis and single-strand conformation polymorphism analysis of the 16S ribosomal DNA, a high degree of moss specificity was found for associated bacterial communities. This specificity could be further evidenced by a cultivation-dependent approach for the following parameters: (i) plate counts of bacteria on R2A medium, (ii) proportion of antagonistic isolates, (iii) antagonistic activity as well as spectrum against pathogens, and (iv) diversity and richness of antagonistic isolates. The proportion of isolates with antagonistic activity against the pathogenic model fungus Verticillium dahliae was highest for S. rubellum (31%), followed by A. palustre (17%) and T. ruralis (5%). A high percentage (99%) of moss-associated antagonistic bacteria produced antifungal compounds. The high recovery of antagonistic isolates strongly suggests that bryophytes represent an ecological niche which harbors a diverse and hitherto largely uncharacterized microbial population with yet unknown and untapped potential biotechnological applications, e.g., for biological control of plant pathogens.     

The influence of snow conditions on the date of breeding of wading birds in north-east Greenland

The young of wading birds that breed in some parts of the arctic hatch when their insect food supply is most abundant. This appears to be the ultimate factor determining the date of egg-laying. In various other arctic birds the date of breeding may be influenced, directly or indirectly, by the time at which snow or ice melts. The Joint Biological Expedition to N.E. Greenland 1974 studied Ringed plovers Charadrius hiaticula , Dunlins Calidris aplina , Sanderlings Calidris alba , Knots Calidris canutus , and Turnstones Arenaria interpres breeding in various areas within 80 km of each other.
In 1974 the thaw was two or three weeks later than normal in the region. The time at which snow cleared and the dates of breeding of the waders differed considerably between valleys: breeding was delayed in valleys that cleared late. In all areas egg-laying ceased early in July, probably because chicks hatching from eggs laid later would not be ready to migrate by the end of the summer. Hence the mean date and length of the egg-laying period were determined by the date of snow clearance from the breeding areas.
Studies of the potential food resources indicate that the waders in N.E. Greenland do not appear to time their breeding so that the young hatch at some peak of food abundance. Sufficient food resources are probably available over a long period of time.     

Bacterial microbiota associated with ants of the genus Tetraponera

Tropical arboreal ants mainly feed as 'secondary herbivores', relying mostly on nitrogen-poor homopteran exudates as food. It has been speculated that this nitrogen-limitation of their diet may be overcome by nutritional upgrading with the help of symbiotic bacteria. We examined the bacterial diversity associated with several representatives of three species groups of the arboreal ant genus Tetraponera based on genes encoding 16S rRNA, citrate synthase and a structural protein of the dinitrogenase complex ( nifH ). The bacterial microflora showed group-specificity, suggesting long-term association between ants and bacteria. In all specimens of four species of the nigra group, we detected bacteria closely related to Bartonella (order Rhizobiales). Ants of the allaborans group harboured bacteria belonging to the enterobacteria. In Tetraponera pilosa of the third species group, we found the enterobacterium Pantoea agglomerans . In spite of the different phylogenetic affiliation of the bacteria identified in the three species groups, the presence of nifH in most species suggests a role in nitrogen metabolism of the bacterial microbiota. We also detected a high infection rate with the intracellular bacterium Wolbachia in all Tetraponera species groups. Besides the widespread bacteria found in Tetraponera , we discovered a diverse group of bacteria represented by single sequences. © 2007 The Linnean Society of London, Biological Journal of the Linnean Society, 2007, 90 , 399–412.     

结直肠癌患者肠道黏膜菌群多样性变化研究

目的应用PCR-DGGE技术对结直肠癌患者肠道黏膜局部菌群多样性进行研究,为结直肠病变的防治提供微生态调节思路。方法收集正常对照组、结直肠息肉组及结直肠癌组患者各30例,采集结直肠黏膜局部肛拭子,提取细菌基因组DNA,采用PCR-DGGE对肠道黏膜局部菌群进行指纹图谱分析。结果正常对照组、结直肠息肉组和结直肠癌组患者PCR-DGGE指纹图谱分析显示3组肠道黏膜局部菌群多样性发生了显著的变化,3组肠道黏膜局部菌群发生了显著的菌群变迁。结论 PCR-DGGE分析结直肠癌患者肠道黏膜局部菌群多样性变化对监测肠道局部微生态变化在结直肠癌的发生过程中的作用具有重要价值。