Metagenomics and the niche concept

Marco, Diana E.

doi:10.1007/s12064-008-0028-x

Cited by 20 publications

(12 citation statements)

References 47 publications

(47 reference statements)

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“…The effects of N fertilization and OM type on nirS ‐denitrifier community structure were always interactive (Table ). These results are consistent with the theory that microbial communities are structured by multidimensional niches (as described by Marco, and Eisenhauer et al ., ). Generally, all the explanations posited above to describe resource regulation of microbial community structure relate to the selection of individual taxa, or whole populations, based upon variations in their ‘trophic strategies’ and the recognition that bacteria have evolved a wide range of capabilities with respect to growth and survival (Tiedje et al ., ; Fierer et al ., ).…”

Section: Discussionsupporting

confidence: 93%

Resource effects on denitrification are mediated by community composition in tidal freshwater wetlands soils

Morrissey

Franklin

2014

Environmental Microbiology

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Accurate prediction of denitrification rates remains difficult, potentially owing to complex uncharacterized interactions between resource conditions and denitrifier communities. To better understand how the availability of organic matter (OM) and nitrate (NO3 (-) ), two of the resources most fundamental to denitrifiers, affect these populations and their activity, we performed an in situ resource manipulation in tidal freshwater wetland soils. Soils were augmented with OM to double ambient concentrations, using either compost or plant litter, and fertilized with KNO3 at two levels (low: ∼ 5 mg l(-1) NO3 (-) -N and high: ∼ 50 mg l(-1) NO3 (-) -N) in a full factorial design. Community composition of nirS-denitrifers (assessed using terminal restriction fragment length polymorphism) was interactively regulated by both NO3 (-) concentration and OM type, and the associated shifts in community composition were relatively consistent across sampling dates (6, 9 and 12 months of incubation). Denitrification potential (pDNF) rates were also strongly affected by NO3 (-) fertilization and increased by ∼ 10-100-fold. Path analysis revealed that the influence of resource availability on pDNF rates was largely mediated through changes in nirS-denitrifier community composition. These results suggest that a greater understanding of denitrifier community ecology may enable more accurate prediction of denitrification rates.

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Section: Discussionsupporting

confidence: 93%

Resource effects on denitrification are mediated by community composition in tidal freshwater wetlands soils

Morrissey

Franklin

2014

Environmental Microbiology

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“…The increase of less dominant bacteria in the absence or reduction of dominant bacteria is a typical mode of action in the development of complex bacterial communities. This model is called "niche concept", although many different definitions of this concept exist [21,22]. It is conceivable that the reduction of dominant members of a bacterial community will lead to the colonization with other members, i.e.…”

Section: Discussionmentioning

confidence: 99%

The Impact of Dietary Zinc Oxide on the Bacterial Diversity of the Small Intestinal Microbiota of Weaned Piglets

Vahjen¹

2014

J Veterinar Sci Technol

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Dietary zinc oxide is often used in pharmacological concentrations to promote health as well as performance of weaned piglets due to its bacteriostatic effects. This study was conducted to provide an in depth analysis of the bacterial composition in weaned piglets fed different amounts of dietary zinc oxide. Piglets were fed diets containing 57 (low), 164 (medium) or 2425 (high) mg/kg dietary zinc. Zinc above the basal dietary level was supplied from analytical grade zinc oxide (ZnO). DNA was extracted from stomach and ileum digesta samples of 32 and 53d old animals (n=4 per group) and used to generate bar-coded 16S ribosomal DNA amplicons for deep sequencing analysis. A total of 9 phyla, 40 orders, 75 families and 328 genera were detected in 8.76 x 10 5 sequencing reads. Firmicutes, Bacteroidetes and Proteobacteria were the dominant phyla, but no significant differences between treatment groups were observed. Lactobacillales (16.3-59.9%), Bacteroidales (2.2-59.1%), Clostridiales (0.05-70.2%) and Selenomonadales (2.6-17.5%) were found as the dominating order. Noteworthy changes on the order level were found for numerically or significantly increased ratios of Clostridiales, but significantly decreased Lactobacillales in the high dietary zinc group. The bacterial diversity for the high dietary zinc diet was significantly higher for the total microbiota than the medium or low zinc diet. However, Lactobacillales diversity decreased, while Clostridiales and Enterobacteriales diversity increased significantly. Principal component analysis confirmed changes in the microbiota, most notably for the high dietary zinc treatment. This study has shown that pharmacological doses of high dietary zinc can drastically alter the bacterial composition and development of the microbiota in weaned piglets. The quantitative shift of bacterial groups due to high dietary zinc was most pronounced one week after weaning, while the more developed microbiota in older animals seemed to be able to adapt to high concentrations of dietary zinc.

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“…Therefore, genetic isolation, rather than parasitism (Zomorodipour and Andersson, 1999; Moran and Wernegreen, 2000; Moran, 2002), has a greater impact on genome reduction. Species complexes may have many different genomic repertoires and can therefore produce alternative phenotypes that are better adapted to their environment (Marco, 2008). According to Lawrence (2002), HGT is the main source of new metabolic abilities for microbial habitat colonization.…”

Section: Sympatric and Allopatric Speciesmentioning

confidence: 99%

Defining Pathogenic Bacterial Species in the Genomic Era

Georgiades¹,

Raoult²

2011

Front. Microbio.

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Actual definitions of bacterial species are limited due to the current criteria of definition and the use of restrictive genetic tools. The 16S ribosomal RNA sequence, for example, has been widely used as a marker for phylogenetic analyses; however, its use often leads to misleading species definitions. According to the first genetic studies, removing a certain number of genes from pathogenic bacteria removes their capacity to infect hosts. However, more recent studies have demonstrated that the specialization of bacteria in eukaryotic cells is associated with massive gene loss, especially for allopatric endosymbionts that have been isolated for a long time in an intracellular niche. Indeed, sympatric free-living bacteria often have bigger genomes and exhibit greater resistance and plasticity and constitute species complexes rather than true species. Specialists, such as pathogenic bacteria, escape these bacterial complexes and colonize a niche, thereby gaining a species name. Their specialization allows them to become allopatric, and their gene losses eventually favor reductive genome evolution. A pathogenic species is characterized by a gene repertoire that is defined not only by genes that are present but also by those that are lacking. It is likely that current bacterial pathogens will disappear soon and be replaced by new ones that will emerge from bacterial complexes that are already in contact with humans.

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Metagenomics and the niche concept

Cited by 20 publications

References 47 publications

Resource effects on denitrification are mediated by community composition in tidal freshwater wetlands soils

Resource effects on denitrification are mediated by community composition in tidal freshwater wetlands soils

The Impact of Dietary Zinc Oxide on the Bacterial Diversity of the Small Intestinal Microbiota of Weaned Piglets

Defining Pathogenic Bacterial Species in the Genomic Era

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