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Understanding how antibiotic resistance emerges and evolves in natural habitats is critical for predicting and mitigating antibiotic resistance in the context of global change. Bacteria have evolved antibiotic production as a strategy to fight competitors, predators and other stressors, but how predation pressure of their most important consumers (i.e., protists) affects soil antibiotic resistance genes (ARGs) profiles is still poorly understood. To address this gap, we investigated responses of soil resistome to varying levels of protistan predation by inoculating low, medium and high concentrations of indigenous soil protist suspensions in soil microcosms. We found that an increase in protistan predation pressure was strongly associated with higher abundance and diversity of soil ARGs. High protist concentrations significantly enhanced the abundances of ARGs encoding multidrug (oprJand ttgBgenes) and tetracycline (tetV) efflux pump by 608%, 724% and 3052%, respectively. Additionally, we observed an increase in the abundance of numerous bacterial genera under high protistan pressure. Our findings provide empirical evidence that protistan predation significantly promotes antibiotic resistance in soil bacterial communities and advances our understanding of the biological driving forces behind the evolution and development of environmental antibiotic resistance.

Soil mosses are among the most widely distributed organisms on land. Experiments and observations suggest that they contribute to terrestrial soil biodiversity and function, yet their ecological contribution to soil has never been assessed globally under natural conditions. Here we conducted the most comprehensive global standardized field study to quantify how soil mosses influence 8 ecosystem services associated with 24 soil biodiversity and functional attributes across wide environmental gradients from all continents. We found that soil mosses are associated with greater carbon sequestration, pool sizes for key nutrients and organic matter decomposition rates but a lower proportion of soil-borne plant pathogens than unvegetated soils. Mosses are especially important for supporting multiple ecosystem services where vascular-plant cover is low. Globally, soil mosses potentially support 6.43 Gt more carbon in the soil layer than do bare soils. The amount of soil carbon associated with mosses is up to six times the annual global carbon emissions from any altered land use globally. The largest positive contribution of mosses to soils occurs under perennial, mat and turf mosses, in less-productive ecosystems and on sandy soils. Our results highlight the contribution of mosses to soil life and functions and the need to conserve these important organisms to support healthy soils.

Understanding how antibiotic resistance emerges and evolves in natural habitats is critical for predicting and mitigating antibiotic resistance in the context of global change. Bacteria have evolved antibiotic production as a strategy to fight competitors, predators and other stressors, but how predation pressure of their most important consumers (i.e., protists) affects soil antibiotic resistance genes (ARGs) profiles is still poorly understood. To address this gap, we investigated responses of soil resistome to varying levels of protistan predation by inoculating low, medium and high concentrations of indigenous soil protist suspensions in soil microcosms. We found that an increase in protistan predation pressure was strongly associated with higher abundance and diversity of soil ARGs. High protist concentrations significantly enhanced the abundances of ARGs encoding multidrug (oprJand ttgBgenes) and tetracycline (tetV)efflux pump by 608%, 724% and 3052%, respectively. Additionally, we observed an increase in the abundance of numerous bacterial genera under high protistan pressure. Our findings provide empirical evidence that protistan predation significantly promotes antibiotic resistance in soil bacterial communities and advances our understanding of the biological driving forces behind the evolution and development of environmental antibiotic resistance.

Soils harbor the most diverse naturally evolved antibiotic resistance genes (ARGs) on Earth, with implications for human health and ecosystem functioning. How ARGs evolve as soils develop over centuries, to millennia (i.e., pedogenesis), remains poorly understood, which introduces uncertainty in predictions of the dynamics of ARGs under changing environmental conditions. Here we investigated changes in the soil resistome by analyzing 16 globally distributed soil chronosequences, from centuries to millennia, spanning a wide range of ecosystem types and substrate age ranges. We show that ARG abundance and diversity decline only after millions of years of soil development as observed in very old chronosequences. Moreover, our data show increases in soil organic carbon content and microbial biomass as soil develops that were negatively correlated with the abundance and diversity of soil ARGs. This work reveals natural dynamics of soil ARGs during pedogenesis and suggests that such ecological patterns are predictable, which together advances our understanding of the environmental drivers of ARGs in terrestrial environments.

Soils harbor the most diverse naturally evolved antibiotic resistance genes (ARGs) on Earth, with implications for human health and ecosystem functioning. How ARGs evolve as soils develop over centuries, to millennia (i.e., pedogenesis), remains poorly understood, which introduces uncertainty in predictions of the dynamics of ARGs under changing environmental conditions. Here we investigated changes in the soil resistome by analyzing 16 globally distributed soil chronosequences, from centuries to millennia, spanning a wide range of ecosystem types and substrate age ranges. We show that ARG abundance and diversity decline only after millions of years of soil development as observed in very old chronosequences. Moreover, our data show increases in soil organic carbon content and microbial biomass as soil develops that were negatively correlated with the abundance and diversity of soil ARGs. This work reveals natural dynamics of soil ARGs during pedogenesis and suggests that such ecological patterns are predictable, which together advances our understanding of the environmental drivers of ARGs in terrestrial environments.

Protists, an integral component of soil microbiome, are one of the main predators of bacteria. Bacteria can produce toxic secondary metabolites, e.g., antibiotics to fight stress under the predation pressure of protists; however, impacts of antibiotics on the profile of protists in soils remain unclear. Here, we constructed a microcosm incubation to investigate the effects of two common antibiotics, oxytetracycline and ciprofloxacin, on the protistan and bacterial communities in an arable soil. Rhizaria were the most abundant protist supergroup, followed by Amoebozoa, Stramenopiles, and Aveolata. Among trophic functional groups, consumers were predominant within the protistan community. The protistan alpha-diversity was not significantly changed, while the bacterial alpha-diversity was decreased under the pressure of antibiotics. Nevertheless, the antibiotic exposure considerably reduced the relative abundance of protistan lineages in Rhizaria and Amoebozoa, which were the dominant supergroups of protistan consumers, while increased the relative abundance of other consumer and phototrophic protists. Altogether, we provide novel experimental evidence that the bacterivorous consumers, an important functional group of protists, were more sensitive to antibiotics than other functional groups. Our findings have potential implications for the induced alterations of protistan community and their ecological functions under the scenarios of projected increasing global antibiotic usage.

The booming application of manufactured nanoparticles raises concerns about their unintentional environmental consequences, one of which is whether nanoparticles will co-selectively enrich soil antibiotic resistance genes (ARGs) which may be transferred to human pathogens through the food chain. We examined soil microbial resistance to tetracycline in three agricultural soils after pre-exposure to 0–100 mg kg−1nanoparticulate La2O3, Nd2O3, and Gd2O3for up to 60 days. Rare earth oxide nanoparticle pre-exposure promoted soil microbial antibiotic resistance, as reflected by the decreased effects of tetracycline on soil microbial biomass and activity in nanoparticle-amended soils. Quantification of ARGs by high-capacity quantitative polymerase chain reaction revealed that the enhanced antibiotic resistance was attributed to the increased relative abundance and diversity of total ARGs which targeted all major classes of antibiotics. Among the 168 observed ARGs, 40 ARGs (e.g., 8 for La2O3, 21 for Nd2O3, and 23 for Gd2O3) were significantly enriched in the presence of nanoparticles (e.g., tetracycline and multidrug resistance genes, P< 0.05), indicating the selective pressure imposed by rare earth oxide nanoparticles in promoting the proliferation of antibiotic resistance genes in soil microbial communities. There was a significantly positive correlation between the relative abundance of mobile genetic elements and ARGs (P< 0.05), suggesting that horizontal gene transfer may have aided the spread and proliferation of ARGs in nanoparticle-amended soils. Taken together, these findings demonstrate that nanoparticulate La2O3, Nd2O3, and Gd2O3can aggravate soil microbial antibiotic resistance by enriching ARGs through co-selection and horizontal gene transfer, and thus forewarn of the environmental and health risks of rare earth oxide nanoparticles in soil ecosystems.

Rice consumption is now recognized as an important pathway of human exposure to the neurotoxin methylmercury (MeHg), particularly in countries where rice is a staple food. Although the discovery of a two-gene cluster hgcABhas linked Hg methylation to several phylogenetically diverse groups of anaerobic microorganisms converting inorganic mercury (Hg) to MeHg, the prevalence and diversity of Hg methylators in microbial communities of rice paddy soils remain unclear. We characterized the abundance and distribution of hgcABgenes using third-generation PacBio long-read sequencing and Illumina short-read metagenomic sequencing, in combination with quantitative PCR analyses in several mine-impacted paddy soils from southwest China. Both Illumina and PacBio sequencing analyses revealed that Hg methylating communities were dominated by iron-reducing bacteria (i.e., Geobacter) and methanogens, with a relatively low abundance of hgcA+sulfate-reducing bacteria in the soil. A positive correlation was observed between the MeHg content in soil and the relative abundance of Geobactercarrying the hgcAgene. Phylogenetic analysis also uncovered some hgcABsequences closely related to three novel Hg methylators, Geobacter anodireducens, Desulfuromonassp. DDH964, and Desulfovibriosp. J2, among which G. anodireducenswas validated for its ability to methylate Hg. These findings shed new light on microbial community composition and major clades likely driving Hg methylation in rice paddy soils.

The conversion of natural forests in subtropical regions into plantations or secondary forests has resulted in alterations in soil variables, microbial communities, and microbially-mediated processes, including nitrous oxide (N2O) emissions. However, how forest conversion influences soil N2O reduction and the abundance and community structure of N2O reducing microorganisms remains unclear. Here, we investigated the impact of converting a natural forest to secondary forest, Cunninghamia lanceolataand Pinus massonianaplantations on the abundance and community structure of N2O reducing microorganisms in both bulk soils and aggregates. Compared with secondary forest, plantations had higher soil pH, available phosphorus and moisture content, and lower soil NH4+content, but similar aggregate sizes. Compared with secondary forest, forest conversion into plantations resulted in significantly higher soil N2O reduction rate and increased abundances of nosZI and nosZII in soils and aggregates. The abundance of nosZI was higher than nosZII in all tested soils and had a stronger association with N2O reduction rates, suggesting the greater role of nosZI carrying microorganisms in N2O consumption. Forest conversion had a greater impact on the community composition of nosZI than nosZII, mainly by increasing the relative abundance of alpha- and beta-Proteobacteria, while decreasing gamma-Proteobacteria. However, nosZII carrying microorganisms were exclusively dominated by Gemmatimonadetes and less affected by forest conversion. Taken together, our findings significantly contribute to our understanding of the eco-physiological characteristics of N2O reducing microorganisms and highlight the importance of nosZI carrying microorganisms in N2O consumption in subtropical forest soils.

Population growth and growing demand for livestock products produce large amounts of manure, which can be harnessed to maintain soil sustainability and crop productivity. However, the impacts of excessive manure application on crop yields, nitrogen (N)-cycling processes and microorganisms remain unknown. Here, we explored the effects of 20-years of excessive rates (18 and 27 Mg ha-1yr-1) of pig manure application on peanut crop yields, soil nutrient contents, N-cycling processes and the abundance of N-cycling microorganisms in an acidic Ultisol in summer and winter, compared with none and a regular rate (9 Mg ha-1yr-1) of pig manure application. Long-term excessive pig manure application, especially at the high-rate, significantly increased soil nutrient contents, the abundance of N-cycling functional genes, potential nitrification and denitrification activity, while it had a weaker effect on peanut yield and plant biomass. Compared with manure application, seasonality had a much weaker effect on N-cycling gene abundance. Random forest analysis showed that available phosphorus (AP) content was the primary predictor for N-cycling gene abundance, with significant and positive associations with all tested N-cycling genes. Our study clearly illustrated that excessive manure application would increase N-cycling gene abundance and potential N loss with relatively weak promotion of crop yields, providing significant implications for sustainable agriculture in the acidic Ultisols.

Manganese (Mn) oxides are important components in soils and sediments. Points-of-zero charge (PZC) of three synthetic Mn oxides (birnessite, cryptomelane, and todorokite) were determined by using three classical techniques (potentiometric titration or PT, rapid PT or RPT, and salt titration or ST) and a modified salt titration method with a prolonged equilibration time (ST method with a prolonged equilibration time PST). The same methods have been applied to goethite, which was used as a reference material. The PZC values of goethite obtained by PT and RPT methods were both 7.95, and those by the ST and PST method were 8.16 and 8.30, respectively, for birnessite cryptomelane, and todorokite. The PT method yielded PZC of 1.18, 1.98, and 3.98, and the RPT method yielded 1.60, 2.11, and 3.47, respectively, for birnessite, cryptomelane, and todorokite. In contrast to goethite, there was no PZC found with the ST method, even when the types and concentrations of the added electrolytes changed. However, when after KCl addition the equilibration time was prolonged 28 h, the PZC of birnessite, cryptomelane, and todorokite could be found and were 0.97, 1.74, and 3.39, respectively. The fact that the normal ST method failed for the Mn oxides is due to their low PZC, because at this low pH value, the oxides may start to dissolve. Compared with PT and RPT methods, the PST method is reliable, simple, and convenient. The PST approach seems also suitable for other similar colloid systems.

Pot experiments were conducted to investigate the effect of soil water regimes on the formation of iron Fe plaque on the root surface of rice seedlings Oryza sativaL. and on the microbial functional diversity in a paddy soil. The rice seedlings were subjected to three moisture regimes submergence, 100, and 60 water-holding capacity WHC, and were grown for 5 and 11 weeks. Aerobic lithotrophic FeII-oxidizing FeOB and acetate-utilizing FeIII-reducing bacteria FeRB in the rhizosphere and non-rhizosphere soil were determined at 5 weeks using the most probable number MPN method. The carbon substrate use patterns of the microbial communities in the rhizosphere and non-rhizosphere soil samples were determined at 11 weeks using Biolog-GN2 plates. The amount of Fe plaque per unit dry root weight was much higher under submerged conditions than at lower soil moisture contents and decreased with plant age. There was a positive correlation between the amount of Fe plaque and phosphorus accumulated in the Fe plaque at both sampling times r = 0.98 and 0.92, respectively, n = 12. Numbers of FeOB and FeRB in the submerged soil were lower than in aerobic soil, but by two orders of magnitude higher in the rhizosphere than in the bulk soil. On the other hand, the functional diversity of the rhizosphere microbial communities was much higher than that of the non-rhizosphere soil, irrespective of soil water regimes. We conclude that soil flooding results in a decreased number and diversity of Fe-oxidizing/reducing bacteria, while increasing the Fe-plaque formation.

Todorokite is a common Mn oxide (with a tunnel structure) in the Earth surface environment, and can be obtained by hydrothermal treatment or refluxing process from precursor buserite with a layered structure. Several chemical reaction conditions for the phase transformation from Na-buserite to todorokite at atmospheric pressure were investigated, including temperature, pH, crystallinity of precursor Na-buserite, the amount of the interlayer Mg2+of the Mg-buserite and clay minerals. The results showed that the conversion rate and crystallinity of todorokite decreased with falling temperature, and Mg-buserite could not be completely transformed to todorokite at lower temperatures (40°C). The poorly crystalline Na-buserite could be converted into todorokite more easily than highly crystalline Na-buserite. Todorokite can be prepared at pH 5–9, but the rate of conversion and crystallinity of todorokite did vary with pH in the order: neutral ≈ alkali > acidic. The conversion rate of todorokite decreased with decreasing interlayer Mg2+content of the Mg-buserite. The presence of montmorillonite or goethite slowed the formation reaction of todorokite in the refluxing process, and the reaction time was prolonged when the amounts of those minerals were increased.

Honeybees provide crucial pollination services and valuable apiarian products. The symbiotic intestinal communities facilitate honeybee health and fitness by promoting nutrient assimilation, detoxifying toxins, and resisting pathogens.