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Abstract Background At lower concentrations copper (Cu), zinc (Zn) and nickel (Ni) are trace metals essential for some bacterial enzymes. At higher concentrations they might alter and inhibit microbial functioning in a bioreactor treating wastewater. We investigated the effect of incremental concentrations of Cu, Zn and Ni on the bacterial community structure and their metabolic functions by shotgun metagenomics. Metal concentrations reported in previous studies to inhibit bacterial metabolism were investigated. Results At 31.5 μM Cu, 112.4 μM Ni and 122.3 μM Zn, the most abundant bacteria were Achromobacter and Agrobacterium. When the metal concentration increased 2 or fivefold their abundance decreased and members of Delftia, Stenotrophomonas and Sphingomonas dominated. Although the heterotrophic metabolic functions based on the gene profile was not affected when the metal concentration increased, changes in the sulfur biogeochemical cycle were detected. Despite the large variations in the bacterial community structure when concentrations of Cu, Zn and Ni increased in the bioreactor, functional changes in carbon metabolism were small. Conclusions Community richness and diversity replacement indexes decreased significantly with increased metal concentration. Delftia antagonized Pseudomonas and members of Xanthomonadaceae. The relative abundance of most bacterial genes remained unchanged despite a five-fold increase in the metal concentration, but that of some EPS genes required for exopolysaccharide synthesis, and those related to the reduction of nitrite to nitrous oxide decreased which may alter the bioreactor functioning.

ABSTRACT The maternal transmission of microbiota during embryonic development of vertebrates is still poorly understood. Here, we used high-throughput sequencing of the 16S rRNA bacterial genes to determine the bacterial communities in the gastrointestinal tract and amniotic environment, i.e., the amniotic fluid, amniotic membrane and extraembryonic yolk, of embryos at the last stage of development of the viviparous lizard Sceloporus grammicus Wiegmann, 1828. We compared these communities to those found in the maternal intestine, mouth, cloaca, and the aseptic ventral skin as a control of the aseptic technique. Our results showed that bacterial 16S rRNA genes were present in the embryos of S. grammicus. Their diversity was lower and more similar in composition between individuals than those found in the maternal tissues. This suggests that a strong control exists on the transmission of bacteria from the mother to the embryos. We found 78% of the embryonic amplicon sequence variants (ASVs) in the maternal bacterial microbiota, suggesting that the transmission of bacteria from the mother to the embryos is a continuous process and some bacteria may have been transferred during early embryonic stages. The embryonic bacteria were found to overlap mostly with those found in the mouth and aseptic ventral skin of the mother, although it is difficult to conclude that the shared ASVs originated from these maternal tissues. Our study provides evidence of microbiota vertical transfer during embryonic development in the animal kingdom. It also highlights that this maternal transmission could be included in the maternal effects that impact the offspring. IMPORTANCE We investigated the presence and diversity of bacteria in the embryos of the viviparous lizard Sceloporus grammicus and their amniotic environment. We compared this diversity to that found in the maternal intestine, mouth, and cloaca. We detected bacterial DNA in the embryos, albeit with a lower bacterial species diversity than found in maternal tissues. Most of the bacterial species detected in the embryos were also found in the mother, although not all of them. Interestingly, we detected a high similarity in the composition of bacterial species among embryos from different mothers. These findings suggest that there may be a mechanism controlling the transmission of bacteria from the mother to the embryo. Our results highlight the possibility that the interaction between maternal bacteria and the embryo may affect the development of the lizards.

Heavy metals are necessary at low concentration for biological activity, but they are often toxic for microorganisms at high concentrations. Amplicon sequencing of 16S rRNA and 18S rRNA was used to investigate changes in the bacterial and microeukaryotic communities in an activated sludge bioreactor incrementally contaminated with nickel (Ni), copper (Cu), and zinc (Zn) with an IC50 value ranging from 0% to 100%, as previously determined, while an uncontaminated bioreactor served as a control. The chemical oxygen demand (COD) was on average 90% in the uncontaminated bioreactor but dropped to 49% when the heavy metal concentration was 100% IC50. The bacterial community in the uncontaminated bioreactor was dominated by Alphaproteobacteria (mostly Agrobacterium and Brevundimonas) when the heavy metal concentrations were low and Bacteroidetes (mostly Sphingobacterium) when the highest amounts of heavy metal concentrations were applied. The members of Ciliophora, Ascomycota, and Basidiomycota alternatively dominated in the uncontaminated bioreactor, while Ascomycota (mostly Fusarium) dominated in the contaminated bioreactor. The results revealed that increased concentrations of Ni, Cu, and Zn altered the bacterial and microeukaryotic communities and some putative metabolic functions.

Abstract Background High-altitude ecosystems are extreme environments that generate specific physiological, morphological, and behavioral adaptations in ectotherms. The shifts in gut microbiota of the ectothermic hosts as an adaptation to environmental changes are still largely unknown. We investigated the food ingested and the bacterial, fungal, and protistan communities in feces of the lizard Sceloporus grammicus inhabiting an altitudinal range using metabarcoding approaches. Results The bacterial phyla Bacteroidetes and Firmicutes, and the genera Bacteroides and Parabacteroides dominated the core fecal bacteriome, while Zygomycota and Ascomycota, and the species Basidiobolus ranarum and Basidiobolus magnus dominated the core fecal mycobiome. The diet of S. grammicus included 29 invertebrate families belonging to Arachnida, Chilopoda, and Insecta. The diversity and abundance of its diet decreased sharply at high altitudes, while the abundance of plant material and Agaricomycetes was significantly higher at the highest site. The composition of the fecal microbiota of S. grammicus was different at the three altitudes, but not between females and males. Dietary restriction in S. grammicus at 4150 m might explain the high fecal abundance of Akkermansia and Oscillopira, bacteria characteristic of long fasting periods, while low temperature favored B. magnus. A high proportion of bacterial functions were digestive in S. grammicus at 2600 and 3100, while metabolism of aminoacids, vitamins, and key intermediates of metabolic pathways were higher at 4150 m. Different assemblages of fungal species in the lizard reflect differences in the environments at different elevations. Pathogens were more prevalent at high elevations than at the low ones. Conclusions Limiting food resources at high elevations might oblige S. grammicus to exploit other food resources and its intestinal microbiota have degradative and detoxifying capacities. Sceloporus grammicus might have acquired B. ranarum from the insects infected by the fungus, but its commensal relationship might be established by the quitinolytic capacities of B. ranarum. The mycobiome participate mainly in digestive and degradative functions while the bacteriome in digestive and metabolic functions.

Land-use change is one of the most important drivers of change in biodiversity. Deforestation for grazing or agriculture has transformed large areas of temperate forest in the central highlands of Mexico, but its impact on soil fungal communities is still largely unknown. In this study, we determined how deforestation of a high-altitude temperate forest for cultivation of maize (Zea mays L.) or husbandry altered the taxonomic, phylogenetic, functional, and beta diversity of soil fungal communities using a 18S rRNA metabarcoding analysis. The true taxonomic and phylogenetic diversity at order q = 1, i.e., considering frequent operational taxonomic units, decreased significantly in the arable, but not in the pasture soil. The beta diversity decreased in the order forest > pasture > arable soil. The ordination analysis showed a clear effect of intensity of land-use as the forest soil clustered closer to pasture than to the arable soil. The most abundant fungal phyla in the studied soils were Ascomycota, Basidiomycota, and Mucoromycota. Deforestation more than halved the relative abundance of Basidiomycota; mostly Agaricomycetes, such as Lactarius and Inocybe. The relative abundance of Glomeromycota decreased in the order pasture > forest > arable soil. Symbiotrophs, especially ectomycorrhizal fungi, were negatively affected by deforestation while pathotrophs, especially animal pathogens, were enriched in the pasture and arable soil. Ectomycorrhizal fungi were more abundant in the forest soil as they are usually associated with conifers. Arbuscular mycorrhizal fungi were more abundant in the pasture than in the arable soil as the higher plant diversity provided more suitable hosts. Changes in fungal communities resulting from land-use change can provide important information for soil management and the assessment of the environmental impact of deforestation and conversion of vulnerable ecosystems such as high-altitude temperate forests.