Effect of Olive Cake and Cactus Cladodes Incorporation in Goat Kids’ Diet on the Rumen Microbial Community Profile and Meat Fatty Acid Composition

The olive cake (OC) and the cactus cladodes (CC) are two alternative feed resources widely available in the southern Mediterranean region that could be used in ruminants’ diet. Their impact on the rumen bacterial ecosystem is unknown. This work aims to evaluate their effects on the microbial community and meat fatty acids of goat’s kids. Forty-four goat kids were divided into four groups receiving diets with conventional concentrate, or 35% OC, or 30% CC, or 15% OC, and 15% CC. After 3 months, these animals were slaughtered, and the rumen liquor and longissimus dorsi and semimembranosus muscles samples were collected. Animals receiving a control diet had rumen liquor with high acidity than test groups (p < 0.001). Test rumen liquor was more adapted to digest efficiently their matching diet than control liquor (p < 0.05). These feedstuffs did not affect rumen bacteria abundance and alpha diversity (richness, evenness, and reciprocal Simpson indexes), and these results were confirmed by beta-diversity tests (NMDS plot, HOMOVA, PERMANOVA). The test diets slightly affected the individual fatty acids of meat (p < 0.05) without effect on fatty acids summaries, indexes, and ratios. Thus, these alternative feed resources could take place in goat kids’ diet to diversify their feed and to reduce feed costs.

Benchmarking laboratory processes to characterise low-biomass respiratory microbiota

The low biomass of respiratory samples makes it difficult to accurately characterise the microbial community composition. PCR conditions and contaminating microbial DNA can alter the biological profile. The objective of this study was to benchmark the currently available laboratory protocols to accurately analyse the microbial community of low biomass samples. To study the effect of PCR conditions on the microbial community profile, we amplified the 16S rRNA gene of respiratory samples using various bacterial loads and different number of PCR cycles. Libraries were purified by gel electrophoresis or AMPure XP and sequenced by V2 or V3 MiSeq reagent kits by Illumina sequencing. The positive control was diluted in different solvents. PCR conditions had no significant influence on the microbial community profile of low biomass samples. Purification methods and MiSeq reagent kits provided nearly similar microbiota profiles (paired Bray–Curtis dissimilarity median: 0.03 and 0.05, respectively). While profiles of positive controls were significantly influenced by the type of dilution solvent, the theoretical profile of the Zymo mock was most accurately analysed when the Zymo mock was diluted in elution buffer (difference compared to the theoretical Zymo mock: 21.6% for elution buffer, 29.2% for Milli-Q, and 79.6% for DNA/RNA shield). Microbiota profiles of DNA blanks formed a distinct cluster compared to low biomass samples, demonstrating that low biomass samples can accurately be distinguished from DNA blanks. In summary, to accurately characterise the microbial community composition we recommend 1. amplification of the obtained microbial DNA with 30 PCR cycles, 2. purifying amplicon pools by two consecutive AMPure XP steps and 3. sequence the pooled amplicons by V3 MiSeq reagent kit. The benchmarked standardized laboratory workflow presented here ensures comparability of results within and between low biomass microbiome studies.

Hydrologic Alteration and Enhanced Microbial Reductive Dissolution of Fe(III) (hydr)oxides Under Flow Conditions in Fe(III)-Rich Rocks: Contribution to Cave-Forming Processes

Previous work demonstrated that microbial Fe(III)-reduction contributes to void formation, and potentially cave formation within Fe(III)-rich rocks, such as banded iron formation (BIF), iron ore and canga (a surficial duricrust), based on field observations and static batch cultures. Microbiological Fe(III) reduction is often limited when biogenic Fe(II) passivates further Fe(III) reduction, although subsurface groundwater flow and the export of biogenic Fe(II) could alleviate this passivation process, and thus accelerate cave formation. Given that static batch cultures are unlikely to reflect the dynamics of groundwater flow conditions in situ, we carried out comparative batch and column experiments to extend our understanding of the mass transport of iron and other solutes under flow conditions, and its effect on community structure dynamics and Fe(III)-reduction. A solution with chemistry approximating cave-associated porewater was amended with 5.0 mM lactate as a carbon source and added to columns packed with canga and inoculated with an assemblage of microorganisms associated with the interior of cave walls. Under anaerobic conditions, microbial Fe(III) reduction was enhanced in flow-through column incubations, compared to static batch incubations. During incubation, the microbial community profile in both batch culture and columns shifted from a Proteobacterial dominance to the Firmicutes, including Clostridiaceae, Peptococcaceae, and Veillonellaceae, the latter of which has not previously been shown to reduce Fe(III). The bacterial Fe(III) reduction altered the advective properties of canga-packed columns and enhanced permeability. Our results demonstrate that removing inhibitory Fe(II) via mimicking hydrologic flow of groundwater increases reduction rates and overall Fe-oxide dissolution, which in turn alters the hydrology of the Fe(III)-rich rocks. Our results also suggest that reductive weathering of Fe(III)-rich rocks such as canga, BIF, and iron ores may be more substantial than previously understood.

Bovine host genome acts on specific metabolism, communication and genetic processes of rumen microbes host-genomically linked to methane emissions

Whereas recent studies in different species showed that the host genome shapes the microbial community profile, our new research strategy revealed substantial host genomic control of comprehensive functional microbial processes in the rumen of bovines by utilising microbial gene profiles from whole metagenomic sequencing. Of 1,107/225/1,141 rumen microbial genera/metagenome assembled uncultured genomes (RUGs)/genes identified, 203/16/352 were significantly (P<2.02 x10-5) heritable (0.13 to 0.61), revealing substantial variation in host genomic control. We found 29/22/115 microbial genera/RUGs/genes host-genomically correlated (-0.93 to 0.92) with emissions of the potent greenhouse gas methane (CH4), highlighting the strength of host genomic control of specific microbial processes impacting on CH4. Only one of these microbial genes was directly involved in methanogenesis (cofG), whereas others were involved in providing substrates for archaea (e.g. bcd and pccB), important microbial interspecies communication mechanisms (ABC.PE.P), host-microbiome interaction (TSTA3) and genetic information processes (RP-L35). In our population, selection based on abundances of the 30 most informative microbial genes provided a mitigation potential of 17% of mean CH4 emissions per generation, which is higher than for selection based on measured CH4 using respiration chambers (13%), indicating the high potential of microbiome-driven breeding to cumulatively reduce CH4 emissions and mitigate climate change.

Effects of influent composition on biological activity, acclimation time and microbial community profile of activated sludge

Background: The performance and stability of activated sludge (AS) processes are strongly related to influent wastewater characteristics. Objective: To investigate the influence of different chemical compositions of influent wastewater, in terms of source of carbon, on activated sludge. Methods: Response was measured in oxygen uptake rate (OUR), volatile suspended solids in the mixed liquor (MVLSS), chemical oxygen demand (COD), and microbial community profile, obtained using Matrix-Assisted Laser Desorption Ionization-Time-of-Flight Mass Spectrometry (MALDI-TOF MS). Results: Results showed that the microbial community profile obtained in both reactors is consistent with those reported for full-scale AS bioreactors treating sewage. However, when the source of carbon is less bioavailable (bioreactor 1), there was a statistically significant difference (p-value<0.05, 95% confidence) in the biological activity of the biomass, both in terms of MLVSS growth and OUR in comparison with the reactor with source of carbon more bioavailable (bioreactor 2). This difference also impacted the time required for complete acclimation: it could be considered completed in 15 days in bioreactor 2, whereas in bioreactor 1, acclimation required more than 120 days to be completed, as during this period there was no net biomass growth even though there was high COD removal.

The Potential Effect of Oral Bacterial Community in Melanophryniscus Admirabilis (Admirable Red-Belly Toads) Conservation

Melanophryniscus admirabilis (admirable red-belly toad) is a microendemic and critically endangered species found exclusively along 700 meters of the Forqueta River, in a fragment of Atlantic Forest in southern Brazil. One of the greatest concerns regarding the conservation of this species is the extensive use of pesticides in areas near their natural habitat. In recent years, the adaptation and persistence of animal species in impacted environments have been associated with microbiota. Therefore, the current study aimed to characterize the oral bacterial community of wild M. admirabilis and to address the question of how this community might contribute to toad&rsquo;s adaptation in the anthropogenic environment and its general metabolic capabilities. In the present study, 11 oral samples collected from wild M. admirabilis were characterized and analyzed via high-throughput sequencing. A total of 181,350 sequences were obtained, resulting in 16 phyla, 34 classes, 39 orders, and 77 families. Proteobacteria dominated (53%) the oral microbiota of toads followed by Firmicutes (18%), Bacteroidetes (17%), and Actinobacteria (5%). No significant differences in microbial community profile from among the samples were reported, suggesting that the dietary restriction may directly influence the bacterial composition. Functional inference of microbiome was performed using PICRUSt2 and important pathways, such as xenobiotic degradation pathways to pesticides and aromatic phenolic compounds were detected, suggesting that the bacterial communities may have important roles in M. admirabilis health and survival in the anthropogenic environment. Overall, our results have important implications for the conservation and management of this microendemic and critically endangered species.