Some bacterial taxa when stimulated by water additions will break dormancy, grow, and become dominant members of the community and contribute significant pulses of CO2 associated with the rewetting event. These pulses of activity are associated with high levels of bacterial productivity in soils. (Aanderud et al. 2011) We examined the bacterial taxa that resuscitate and become metabolically active following two forms of water stress (soil drying-rewetting and freeze-thaw cycles) and we captured and measured the CO2 emanating from those soils. Specifically, We used target metagenomics, which uses a specific gene pool within bacteria that is associated with a function of an ecological process, in this case active (16S rRNA communities) bacteria and all bacteria (16S rRNA communities) during drying-rewetting and freeze-thaw cycles. We measured an array of community dynamics (i.e., evenness, richness, diversity, relative abundance of taxa, and network analyses between taxa) as dry soils are rewetted and as frozen soils thaw multiple times in three cold desert soils. Soils from all three locations exhibited some similar bacterial taxa and gene function but were large in part their own community derived from the evolutionary history of the continent in which they reside.

In arid and semi-arid ecosystems, dominant tree species create dramatic mosaics of plant islands of fertility and relatively barren plant interspaces that exert immense pressure on ecosystem processes and offers an ideal opportunity to explore the impact of bacterial communities. We evaluated potential links between soil respiration and N mineralization, and community co-occurrence networks and predicted gene function across three tree island microsites (i.e., beneath tree canopies, at the canopy edge, and in interspaces) in a replicated field experiment in thirty-eight woodlands sites in the Great Basin Desert in UT, USA. Additionally, we potentially intensified the effects of tree islands by creating a treatment where whole trees were shredded and the resulting fine woody debris (FWD) was deposited onto the soil surface and measured a suite of characteristics relating to the metabolic functional state of communities (i.e., microbial efficiency as the microbial quotient, C substrate quality, biomass, and dissolved organic C) to improve our interpretation of potential links between function and structure. We found that tree islands were the predominant driver, creating highly complex and connected assemblies of bacterial populations and easily discernable differences in abundance and composition of predicted functional genes. Specifically, communities directly beneath Juniperus and Pinus canopies were comprised of at least 5.2-times more connections between bacterial taxa than present in networks from interspace and edge. Using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) to predict the gene expression, differences in the functional potential mirrored shifts in network complexity. Tree island communities expressed 236 genes with many related to the degradation of polyaromatic or polycyclic compounds, while interspace communities expressed only 66 genes associated with the decomposition of more labile C substrates. We observed a robust tree island microsite effect on all ecosystem processes, with soil respiration rates increasing 12% and N mineralization decreasing 29% in canopy than interspace soils demonstrating that a more recalcitrant substrate from a sole C source provided high amounts of low quality of DOC and lead to a decrease in metabolic efficiency, but ultimately selected for a specific community assembly. Alternatively, communities at the edge of canopies, experiencing both tree island and interspace soil conditions generated similar levels of soil respiration as canopy soils regardless of not selecting for a highly connected community and/or specific genes suggesting that a diverse composition of labile and recalcitrant C substrates from multiple sources (e.g., trees, perennial grasses, annual grasses, and forbs) potentially elevates function by promoting the activity of a wide range of taxa. Our results identify that tree islands exert enough pressure to create distinct interactions between bacteria and alter gene expression resulting in changes in ecosystem function, but the link between structure and function is mediated through the diversity and quality of C substrates.

Soluble dietary fibers (SDF) are fermented more than insoluble dietary fibers (IDF), but their effect on colonic bacterial community structure and function remains unclear. Thus, bacterial community composition and function in the colon of BALB/c mice (n = 7) fed with a high level (approximately 20%) of typical SDF, oat-derived beta-glucan (G), microcrystalline cellulose (M) as IDF, or their mixture (GM), were compared. Mice in group G showed a lowest average feed intake (p < 0.05) but no change on the average body weight gain (p > 0.05) compared to other groups, which may be associated with the highest concentration of colonic propionate (p < 0.05) in these mice. The bacterial alpha-diversity of group G was significantly lower than other groups (p < 0.01). In group G, the relative abundance of bacteria belonging to the phylum Bacteroidetes was significantly increased, whereas bacteria from the phylum Firmicutes were significantly decreased (p < 0.01). The core bacteria for different treatments showed distinct differences. Bacteroides, Dehalobacterium, and Prevotella, including known acetogens and carbohydrate fermenting organisms, were significantly increased in relative abundance in group G. In contrast, Adlercreutzia, Odoribacter, and Coprococcus were significantly more abundant in group M, whereas Oscillospira, Desulfovibrio, and Ruminoccaceae, typical hydrogenotrophs equipped with multiple carbohydrate active enzymes, were remarkably enriched in group GM (p < 0.05). The relative abundance of bacteria from the three classes of Proteobacteria, Betaproteobacteria, Gammaproteobacteria (including Enterobacteriaceae) and Deltaproteobacteria, were significantly more abundant in group G, indicating a higher ratio of conditional pathogenic bacteria in mice fed dietary beta-glucan in current study. The predicted colonic microbial function showed an enrichment of "Energy metabolism" and "Carbohydrate metabolism" pathways in mice from group G and M, suggesting that the altered bacterial community in the colon of mice with the two dietary fibers probably resulted in a more efficient degradation of dietary polysaccharides. Our result suggests that the influence of dietary beta-glucan (SDF) on colonic bacterial community of mice was more extensively than MCC (IDF). Co-supplementation of the two fibers may help to increase the bacterial diversity and reduce the conditional pathogens in the colon of mice.

Ľudské telo je prostredím pre život neuveriteľného množstva mikróbov. Niektoré z nich môžu spôsobovať rôzne choroby, ale ďalšie, napríklad črevný mikrobióm, sú pre život a zdravie človeka nepostrádateľné. Nanešťastie, črevný mikrobióm nie je detailne preštudovaný, pretože obsahuje tisíce rôznych druhov baktérií, z ktorých väčšina sa nedá kultivovať v laboratórnych podmienkach. Riešením tohto problému sú nové rýchle metódy sekvenovania v kombináciou s bioinformatickými nástrojmi na výpočet funkčného profilu baktérií vo vzorke. V tejto práci si predstavíme existujúce nástroje predpovedajúce funkčný profil, a následne navrhneme nový nástroj, ktorý môže implementovať konsenzus nad výsledkami existujúcich nástrojov, alebo sa môže jednať o úplne nový nástroj.

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