Molecular microbial ecology of the gastrointestinal tract: from phylogeny to function

During the past decade it became evident that anaerobic cultivation-based approaches provides an incomplete picture of the microbial diversity in the GI tract, since at present only a minority of microbes can be obtained in culture. The application of molecular, mainly 16S ribosomal RNA (rRNA)-based approaches enables researchers to bypass the cultivation step and has proven its usefulness in studying the microbial composition in a variety of ecosystems, including the gastrointestinal (GI) tract. This critical review summarizes the impact of these culture-independent approaches on our knowledge of the ecology of the GI tract and provides directions for future studies which should emphasize function of specific strains, species and groups of microbes.     

Linkage of microbial ecology to phenotype: correlation of rumen microbial ecology to cattle's feed efficiency

Linkage of rumen microbial structure to host phenotypical traits may enhance the understanding of host-microbial interactions in livestock species. This study used culture-independent PCR-denaturing gradient gel electrophoresis (PCR-DGGE) to investigate the microbial profiles in the rumen of cattle differing in feed efficiency. The analysis of detectable bacterial PCR-DGGE profiles showed that the profiles generated from efficient steers clustered together and were clearly separated from those obtained from inefficient steers, indicating that specific bacterial groups may only inhabit in efficient steers. In addition, the bacterial profiles were more likely clustered within a certain breed, suggesting that host genetics may play an important role in rumen microbial structure. The correlations between the concentrations of volatile fatty acids and feed efficiency traits were also observed. Significantly higher concentrations of butyrate (P < 0.001) and valerate (P = 0.006) were detected in the efficient steers. Our results revealed potential associations between the detectable rumen microbiota and its fermentation parameters with the feed efficiency of cattle.     

A view on microbial ecology

World Journal of Microbiology and Biotechnology - In the research areas referred to above the Department of General Microbiology in Copenhagen is involved directly or indirectly. Microbial ecology...     

Multivariate analyses in microbial ecology

Environmental microbiology is undergoing a dramatic revolution due to the increasing accumulation of biological information and contextual environmental parameters. This will not only enable a better identification of diversity patterns, but will also shed more light on the associated environmental conditions, spatial locations, and seasonal fluctuations, which could explain such patterns. Complex ecological questions may now be addressed using multivariate statistical analyses, which represent a vast potential of techniques that are still underexploited. Here, well-established exploratory and hypothesis-driven approaches are reviewed, so as to foster their addition to the microbial ecologist toolbox. Because such tools aim at reducing data set complexity, at identifying major patterns and putative causal factors, they will certainly find many applications in microbial ecology.     

The maturing of microbial ecology.

A.J. Kluyver and C.B. van Niel introduced many scientists to the exceptional metabolic capacity of microbes and their remarkable ability to adapt to changing environments in The Microbe's Contribution to Biology. Beyond providing an overview of the physiology and adaptability of microbes, the book outlined many of the basic principles for the emerging discipline of microbial ecology. While the study of pure cultures was highlighted, provided a unifying framework for understanding the vast metabolic potential of microbes and their roles in the global cycling of elements, extrapolation from pure cultures to natural environments has often been overshadowed by microbiologists inability to culture many of the microbes seen in natural environments. A combination of genomic approaches is now providing a culture-independent view of the microbial world, revealing a more diverse and dynamic community of microbes than originally anticipated. As methods for determining the diversity of microbial communities become increasingly accessible, a major challenge to microbial ecologists is to link the structure of natural microbial communities with their functions. This article presents several examples from studies of aquatic and terrestrial microbial communities in which culture and culture-independent methods are providing an enhanced appreciation for the microbe's contribution to the evolution and maintenance of life on Earth, and offers some thoughts about the graduate-level educational programs needed to enhance the maturing field of microbial ecology.     

The microbial ecology of the Great Salt Lake

The Great Salt Lake is actually two lakes. A highly saline (330-gml^–1) northern arm and a moderately saline (120-gml^–1) southern arm separated by a semipermeable rock causeway. The lake, particularly the northern arm, has a massive accumulation of organic matter resulting from more than 100,000 years of productivity, cycling from a freshwater to a saline lake, plus the influence of human industry and agriculture in more recent times. The north arm planktonic and attached community consists principally of, in order of biomass: bacteria of at least two genera,Halobacterium andHalococcus; two algae,Dunaliella salina andD. viridis; the brine shrimp,Anemia salina; and, two species of brine fly,Ephydra gracilis andE. hians and possibly one more species. The algae and the bacteria appear to depend on each other for nutrients. The bacteria use organic matter produced by the algae and the algae use ammonia produced by the bacteria and possibly the brine shrimp. The production of ammonia appears to be the rate-limiting step although there is no shortage of other forms of nitrogen in the north arm. Based on aquarium studies, the potential for biomass production of algae and bacteria is much higher than actually observed in the north arm, leading to the postulation of two additional factors controlling population; the grazing of the algae by invertebrates with the excretion of compounds rich in nitrogen, and the effect of a low habitat temperature and winter cold on the bacteria, reducing their metabolic activities to nearly zero. Some aspects of the various organisms and their metabolism are discussed. A comparison is made with recent work on the Dead Sea.     

PCR-DGGE技术及其在微生物生态学中的应用

现代分子生物学技术PCR-DGGE是一种分析微生物群落的有效工具,可以用于研究生态系统中微生物多样性和群落动态性。本文简要介绍了PCR-DGGE技术原理及其在微生物生态学领域的应用,并对该技术的局限性进行了评价。     

Tales from the tomb: the microbial ecology of exposed rock surfaces

Although a broad diversity of eukaryotic and bacterial taxa reside on rock surfaces where they can influence the weathering of rocks and minerals, these communities and their contributions to mineral weathering remain poorly resolved. To build a more comprehensive understanding of the diversity, ecology and potential functional attributes of microbial communities living on rock, we sampled 149 tombstones across three continents and analysed their bacterial and eukaryotic communities via marker gene and shotgun metagenomic sequencing. We found that geographic location and climate were important factors structuring the composition of these communities. Moreover, the tombstone‐associated microbial communities varied as a function of rock type, with granite and limestone tombstones from the same cemeteries harbouring taxonomically distinct microbial communities. The granite and limestone‐associated communities also had distinct functional attributes, with granite‐associated bacteria having more genes linked to acid tolerance and chemotaxis, while bacteria on limestone were more likely to be lichen associated and have genes involved in photosynthesis and radiation resistance. Together these results indicate that rock‐dwelling microbes exhibit adaptations to survive the stresses of the rock surface, differ based on location, climate and rock type, and seem pre‐disposed to different ecological strategies (symbiotic versus free‐living lifestyles) depending on the rock type.