High geogenic soil thallium shows limited impact on bacterial community.

Thallium (Tl) is a highly toxic trace metal, included in the US EPA list of priority pollutants. Even though its toxicity is potentially higher or comparable to Cd or Hg, its environmental impact is largely unknown. Despite its toxicity, only a few recent studies are mapping the impact of recently introduced Tl on soil microbial communities, namely in agricultural systems but no studies focus on its long term effect. To complement the understanding of the impact of Tl on soil, this study aims to describe the influence of extremely high naturally occurring Tl concentration (50 mg/kg of potentially bioavailable Tl) on soil microbial communities. Our investigation concentrated on samples collected at Buus (Erzmatt, Swiss Jura, Switzerland), encompassing forest and meadow soil profiles of the local soil formed on hydrothermally mineralized dolomite rock, which is naturally rich in Tl. The soil profiles showed a significant proportion of potentially bioavailable Tl. Yet, even this high concentration of Tl has a limited impact on the richness of the soil bacterial community. Only the meadow soil samples show a reduced richness compared to control samples. Furthermore, our analysis of geogenic Tl contamination in the region unveiled a surprising finding: compared to other soils of Switzerland and in stark contrast to soils affected by recent mining activities, the structure of the bacterial community in Buus remained relatively unaffected. This observation highlights the unique ability of soil microbial communities to withstand extreme Tl contamination. Our study advances the understanding of Tl's environmental impact and underscores the resilience of soil microbes in the face of severe long-term contamination.

Combined effects of nitrate and medium-chain fatty acids on methane production, rumen fermentation, and rumen bacterial populations in vitro.

This study investigated the combined effects of nitrate (NT) and medium-chain fatty acids (MCFA), including C8, C10, C12, and C14, on methane (CH4) production, rumen fermentation characteristics, and rumen bacteria using a 24 h batch incubation technique. Four types of treatments were used: control (no nitrate, no MCFA), NT (nitrate at 3.65 mM), NT + MCFA (nitrate at 3.65 mM + one of the four MCFA at 500 mg/L), and NT + MCFA/MCFA (nitrate at 3.65 mM + a binary combination of MCFA at 250 and 250 mg/L). All treatments decreased (P < 0.001) methanogenesis (mL/g dry matter incubated) compared with the control, but their efficiency was dependent on the MCFA type. The most efficient CH4 inhibitor was the NT + C10 treatment (- 40%). The combinations containing C10 and C12 had the greatest effect on bacterial alpha and beta diversity and relative microbial abundance (P < 0.001). Next-generation sequencing showed that the family Succinivibrionaceae was favored in treatments with the greatest CH4 inhibition at the expense of Prevotella and Ruminococcaceae. Furthermore, the relative abundance of Archaea decreased (P < 0.05) in the NT + C10 and NT + C10/C12 treatments. These results confirm that the combination of NT with MCFA (C10 and C12 in particular) may effectively reduce CH4 production.

The bifidobacterial distribution in the microbiome of captive primates reflects parvorder and feed specialization of the host.

Bifidobacteria, which commonly inhabit the primate gut, are beneficial contributors to host wellbeing. Anatomical differences and natural habitat allow an arrangement of primates into two main parvorders; New World monkeys (NWM) and Old World monkeys (OWM). The number of newly described bifidobacterial species is clearly elevated in NWM. This corresponds to our finding that bifidobacteria were the dominant group of cultivated gut anaerobes in NWM, while their numbers halved in OWM and were often replaced by Clostridiaceae with sarcina morphology. We examined an extended MALDI-TOF MS database as a potential identification tool for rapid screening of bifidobacterial distribution in captive primates. Bifidobacterial isolates of NWM were assigned mainly to species of primate origin, while OWM possessed typically multi-host bifidobacteria. Moreover, bifidobacterial counts reflected the feed specialization of captive primates decreasing from frugivore-insectivores, gummivore-insectivores, frugivore-folivores to frugivore-omnivores. Amplicon sequencing analysis supported this trend with regards to the inverse ratio of Actinobacteria and Firmicutes. In addition, a significantly higher diversity of the bacterial population in OWM was found. The evolution specialization of primates seems to be responsible for Bifidobacterium abundance and species occurrence. Balanced microbiota of captive primates could be supported by optimized prebiotic and probiotic stimulation based on the primate host.

The effect of reverse transcription enzymes and conditions on high throughput amplicon sequencing of the 16S rRNA.

It is assumed that the sequencing of ribosomes better reflects the active microbial community than the sequencing of the ribosomal RNA encoding genes. Yet, many studies exploring microbial communities in various environments, ranging from the human gut to deep oceans, questioned the validity of this paradigm due to the discrepancies between the DNA and RNA based communities. Here, we focus on an often neglected key step in the analysis, the reverse transcription (RT) reaction. Previous studies showed that RT may introduce biases when expressed genes and ribosmal rRNA are quantified, yet its effect on microbial diversity and community composition was never tested. High throughput sequencing of ribosomal RNA is a valuable tool to understand microbial communities as it better describes the active population than DNA analysis. However, the necessary step of RT may introduce biases that have so far been poorly described. In this manuscript, we compare three RT enzymes, commonly used in soil microbiology, in two temperature modes to determine a potential source of bias due to non-standardized RT conditions. In our comparisons, we have observed up to six fold differences in bacterial class abundance. A temperature induced bias can be partially explained by G-C content of the affected bacterial groups, thus pointing toward a need for higher reaction temperatures. However, another source of bias was due to enzyme processivity differences. This bias is potentially hard to overcome and thus mitigating it might require the use of one enzyme for the sake of cross-study comparison.

Microbial community response to hydration-desiccation cycles in desert soil.

Life in desert soil is marked by episodic pulses of water and nutrients followed by long periods of drought. While the desert flora and fauna flourish after rainfall the response of soil microorganisms remains unclear and understudied. We provide the first systematic study of the role of soil aqueous habitat dynamics in shaping microbial community composition and diversity. Detailed monitoring of natural microbial communities after a rainfall event revealed a remarkable decrease in diversity and a significant transition in community composition that were gradually restored to pre-rainfall values during soil desiccation. Modelling results suggest a critical role for the fragmented aqueous habitat in maintaining microbial diversity under dry soil conditions and diversity loss with wetting events that increase connectivity among habitats. This interdisciplinary study provides new insights into wetting and drying processes that promote and restore the unparalleled microbial diversity found in soil.