SARS-CoV-2 has been found in soil and aquatic environments in addition to aerosols. SARS-CoV-2 enters the soil from various sources, including organic amendments and waste irrigation water. The virus counts and virulence in soil depend on spillover routes and soil properties. Organic matter (OM) and clay minerals protect and enable SARS-CoV-2 to survive for longer periods in soil. Therefore, life forms residing in soil may be at risk, but there is a paucity of scientific interest in such interactions. With this perspective, we aim to provide a new viewpoint on the effects of SARS-CoV-2 on soil microbes. In particular, we present a conceptual model showing how successive mutations within soil animals having the SARS-CoV-2 receptor angiotensin-converting enzyme 2 (ACE2) may change its characteristics and, thus, enable it to infect micro- and macroorganisms and be transferred by them. SARS-CoV-2 particles could be adsorbed on mineral or OM surfaces, and these surfaces could serve as encounter sites for infectious attacks. SARS-CoV-2 accumulation in soil over time can perturb bacteria and other microbes, leading to imbalances in microbial diversity and activities. Thus, SARS-CoV-2 and its interactions with biotic and abiotic soil components should be a future research priority.
Tag: microbial activities
Phyllanthus emblica (Amla) Fruit Powder as a Supplement to Improve Preweaning Dairy Calves’ Health: Effect on Antioxidant Capacity, Immune Response, and Gut Bacterial Diversity
Disease is the main reason for the use of antimicrobials in calf rearing, and antibiotics are commonly used to treat calves, including for unknown diseases. This leads to antimicrobial resistance, which is a challenge to the livestock industry and public health. Plant products containing high levels of phytochemicals may improve the immunity and resistance of calves against infections, thereby reducing the use of antimicrobials. This study aimed to investigate the effect of Phyllanthus emblica (Amla) fruit powder (PE) supplementation on antioxidant capacity and immune response of preweaning dairy calves. One hundred, 2-day-old, male Holstein calves were randomly assigned into five treatment groups receiving 0, 5, 10, 20, and 40 g/d PE supplementation. Antioxidant and immune indices and pro- and anti-inflammatory cytokines were analyzed from serum samples, whereas 16S rRNA was analyzed from rumen fluid and fecal samples. PE supplementation, at 5 g/d, protected calves against oxidative stress and improved antioxidant enzymes and immune and anti-inflammatory responses, showing its immunity-enhancing and protective roles against infections. However, the antioxidant capacity and immune response decreased with increasing PE levels, illustrating the adverse effects of PE supplementation at higher doses. The analysis of ruminal and fecal bacterial community abundance detected higher proportions of Firmicutes at an early age, and a higher Bacteroidetes to Firmicutes ratio at weaning, in calves supplemented with 5 g/d PE. This contributed to the development of the immune system in early life, and improved immune and anti-inflammatory responses at a later age. The overall results suggest that PE could be supplemented at 5 g/d for preweaning dairy calves to protect against oxidative stress and infections while maintaining normal gut microbial hemostasis.
Continental-scale insights into the soil microbial co-occurrence networks of Australia and their environmental drivers
Soil microbial communities and their interactions play a critical role in shaping the functions of ecosystems at regional and continental scales. In recent years, co-occurrence network analyses have provided a way to investigate microbial interactions among different microorganisms. But understanding how different environmental factors shape these networks at the continental scale remains challenging. Analyzing fungal, bacterial, and archaeal data from 166 study sites across Australia, we inferred a meta-community level soil microbial co-occurrence network for the Australian continent. Additionally, we analyzed node-level and network-level topological shifts associated with the five major vegetation types. Our results indicate that soils in the Australian savannah systems harbor a unique microbial association pattern, with the highest proportion of positive linkages, highest modularity and lowest average path length in comparison to soils from other vegetation types. Multi-model approaches revealed that different environmental drivers, including soil properties, temperature, and vegetation type, regulated the spatial distribution of topological parameters of the soil microbial networks analyzed in our study. We further generated high-resolution predication maps of microbial networks for Australia, providing insight into the distribution of soil microbes across the continent. By determining how the microbial co-occurrence networks vary according to vegetation type and mapping the distribution of the key parameters of these networks across Australia, we provide a unique understanding of microbial biogeography at the continental scale.
Enhanced soil quality after forest conversion to vegetable cropland and tea plantations has contrasting effects on soil microbial structure and functions
Land-use changes could potentially exert a strong influence on soil quality and soil microbial communities. Moreover, microbial taxa are also important drivers of soil ecological functions. However, the linkage between soil quality and soil microbial communities is in need of deeper understanding. Here, we examined the effects of soil fertility quality on microbial community structure that identified by pyrosequencing and functions that predicted by the FAPROTAX functional annotations dataset after forest conversion to vegetable cropland and tea plantations. Soil quality index was significantly increased after natural forest (0.2) conversion to vegetable cropland (0.7) and tea plantations (0.3–0.6). Soil bacterial beta diversity significantly correlated to soil quality index, but the sensitivity of individual microbial groups varied in response to changes in soil quality. Higher soil quality promoted bacterial diversity in vegetable cropland but decreased it in tea plantations, which implied soil quality was a structural factor in bacterial community composition but had contrasting effects for croplands versus plantations. Agricultural management played a negative role in maintaining microbial interactions, as identified by the network analysis, and furthermore the analysis revealed key functions of the microbial communities. After land-use change, the abundance (e.g., level, intensity) of microbial groups involved in N-cycling increased in tea plantations but decreased in vegetable cropland. The abundance of microbes involved in C-cycling featured an opposite trend. Higher level of N-fixation in tea plantations but the higher abundance of N-oxidation in vegetable cropland was demonstrated. Higher abundance of ammonia-oxidizing bacteria (8.5 × 104 vs. 0.9–2.4 × 104 copies) and ammonia-oxidizing archaea (3.0 × 105 vs. 0.5–1.0 × 105 copies) as identified by qPCR in cropland than that in plantations corroborated the FAPROTAX prediction. Therefore, the key taxa of soil microbial communities and microbial functions were largely dependent on changes in soil quality and determined responses to specific agricultural management.
Ruminal Microbes Exhibit a Robust Circadian Rhythm and Are Sensitive to Melatonin
Gut hormones are not only able to regulate digestive, absorptive, and immune mechanisms of the intestine through biological rhythms, but impact the host through their interactions with intestinal microorganisms. Whether hormones in ruminal fluid have an association with the ruminal ecology is unknown. Objectives of the study were to examine relationships between the diurnal change in ruminal hormones and microbiota in lactating cows, and their associations in vivo and in vitro. For the in vivo study, six cows of similar weight (566.8 ± 19.6 kg), parity (3.0 ± 0.0), and milk performance (8,398.7 ± 1,392.9 kg/y) were used. They were adapted to natural light for 2 weeks before sampling and fed twice daily at 07:00 a.m. and 14:00 p.m. Serum, saliva, and ruminal fluid samples were collected at 02:00, 10:00, and 18:00 on the first day and 06:00, 14:00, and 22:00 on the second day of the experimental period. The concentrations of melatonin (MLT), growth hormone (GH), and prolactin (PRL) were measured via radioimmunoassay, whereas amplicon sequencing data were used to analyze relative abundance of microbiota in ruminal fluid. JTK_CYCLE analysis was performed to analyze circadian rhythms of hormone concentrations as well as the relative abundance of microbiota. For the in vitro study, exogenous MLT (9 ng) was added into ruminal fluid incubations to investigate the impacts of MLT on ruminal microbiota. The results not only showed that rumen fluid contains MLT, but the diurnal variation of MLT and the relative abundance of 9% of total rumen bacterial operational taxonomic units (OTUs) follow a circadian rhythm. Although GH and PRL were also detected in ruminal fluid, there was no obvious circadian rhythm in their concentrations. Ruminal MLT was closely associated with Muribaculaceae, Succinivibrionaceae, Veillonellaceae, and Prevotellaceae families in vivo. In vitro, these families were significantly influenced by melatonin treatment, as melatonin treatment increased the relative abundance of families Prevotellaceae, Muribaculaceae while it reduced the relative abundance of Succinivibrionaceae, Veillonellaceae. Collectively, ruminal microbes appear to maintain a circadian rhythm that is associated with the profiles of melatonin. As such, data suggest that secretion of melatonin into the rumen could play a role in host-microbe interactions in ruminants. © Copyright © 2021 Ouyang, Wang, Bu, Ma, Liu, Xue, Du, Aboragah and Loor.
Strong priming of soil organic matter induced by frequent input of labile carbon
Labile carbon (C) inputs to soil (e.g., litter and root exudation) can prime soil organic matter (SOM) decomposition, and strongly influence SOM dynamics. The direction and intensity of priming, as well as the net C balance in soil, depend on the amount and frequency of labile C inputs. Most recent priming studies are based on single C additions, which are not truly representative of common litter inputs or root exudation in terrestrial ecosystems. Here, we evaluated the effects of 14C-labeled glucose addition to soil in the same final amounts (360 μg C g−1) split into two temporal patterns: seldom (20% of microbial biomass every two months) and frequent addition (4% of microbial biomass every 10 days) on the dynamics of CO2 production and SOM priming over a 200-day incubation. For the first time, we combined enzyme kinetics with substrate-induced growth respiration and fungal diversity to monitor microbially mediated SOM mineralization in response to the labile C input frequency. Frequent glucose addition decreased 14C incorporation into microbial biomass and almost doubled cumulative priming compared to seldom addition, resulting in a net loss of SOM for seldom and frequent C additions of −94 and −367 μg C g−1 respectively. Larger priming loss of SOM with frequent C inputs was accompanied by increased activities of β-glucosidase, chitinase, and acid phosphatase, and by a shift in fungal community towards increased abundance of K-strategist fungal species (mainly Mortierellales sp. and Trichoderma sp.) capable of SOM mineralization. In conclusion, frequent labile C inputs (e.g., rhizodeposits in rhizosphere or litterfall in disturephere) to soil will stimulate a shift in fungal community structure and functions, resulting in intensive priming of SOM decomposition and CO2 losses. © 2020 Elsevier Ltd
Unraveling consequences of soil micro- and nano-plastic pollution on soil-plant system: Implications for nitrogen (N) cycling and soil microbial activity
Micro- and nano-plastics have widely been recognized as major global environmental problem due to its widespread use and inadequate waste management. The emergence of these plastic pollutants in agroecosystem is a legitimate ecotoxicological concerns for food web exchanges. In agriculture, micro/nano plastics are originated from a variety of different agricultural management practices, such as the use of compost, sewage sludge and mulching. A range of soil properties and plant traits are affected by their presence. With the increase of plastic debris, these pollutant materials have now begun to demonstrate serious implications for key soil ecosystem functions, such as soil microbial activity and nutrient cycling. Nitrogen (N) cycle is key predictor of ecological stability and management in terrestrial ecosystem. In this review, we evaluate ecological risks associated with micro-nano plastic for soil-plant system. We also discuss the consequence of plastic pollutants, either positive or negative, on soil microbial activities. In addition, we systematically summarize both direct and hypothesized implications for N cycling in agroecosystem. We conclude that soil N transformation had showed varied effects resulting from different types and sizes of plastic polymers present in soil. While mixed effects of microplastic pollution on plant growth and yield have been observed, biodegradable plastics have appeared to pose greater risk for plant growth compared to chemical plastic polymers.