More sensitive microbial responses to the interactive effects of warming and altered precipitation in subsoil than topsoil of an alpine grassland ecosystem.

Subsoil is a large organic carbon reservoir, storing more than half of the total soil organic carbon (SOC) globally. Conventionally, subsoil is assumed to not be susceptible to climate change, but recent studies document that climate change could significantly alter subsoil carbon cycling. However, little is known about subsoil microbial responses to the interactive effects of climate warming and altered precipitation. Here, we investigated carbon cycling and associated microbial responses in both subsoil (30-40 cm) and topsoil (0-10 cm) in a Tibetan alpine grassland over 4 years of warming and altered precipitation. Compared to the unchanged topsoil carbon (ß = .55, p = .587), subsoil carbon exhibited a stronger response to the interactive effect of warming and altered precipitation (ß = 2.04, p = .021), that is, warming decreased subsoil carbon content by 28.20% under decreased precipitation while warming increased subsoil carbon content by 18.02% under increased precipitation.Furthermore, 512 metagenome-assembled genomes (MAGs) were recovered, including representatives of phyla with poor genomic representation. Compared to only one changed topsoil MAG, 16 subsoil MAGs were significantly affected by altered precipitation, and 5 subsoil MAGs were significantly affected by the interactive effect of warming and precipitation. More than twice as many populations whose MAG abundances correlated significantly with the variations of carbon content, components and fluxes were observed in the subsoil than topsoil, suggesting their potential contribution in mediating subsoil carbon cycling. Collectively, our findings highlight the more sensitive responses of specific microbial lineages to the interactive effects of warming and altered precipitation in the subsoil than topsoil, and provide key information for predicting subsoil carbon cycling under future climate change scenarios.

GSearch: ultra-fast and scalable genome search by combining K-mer hashing with hierarchical navigable small world graphs.

Genome search and/or classification typically involves finding the best-match database (reference) genomes and has become increasingly challenging due to the growing number of available database genomes and the fact that traditional methods do not scale well with large databases. By combining k-mer hashing-based probabilistic data structures (i.e. ProbMinHash, SuperMinHash, Densified MinHash and SetSketch) to estimate genomic distance, with a graph based nearest neighbor search algorithm (Hierarchical Navigable Small World Graphs, or HNSW), we created a new data structure and developed an associated computer program, GSearch, that is orders of magnitude faster than alternative tools while maintaining high accuracy and low memory usage. For example, GSearch can search 8000 query genomes against all available microbial or viral genomes for their best matches (n = ∼318 000 or ∼3 000 000, respectively) within a few minutes on a personal laptop, using ∼6 GB of memory (2.5 GB via SetSketch). Notably, GSearch has an O(log(N)) time complexity and will scale well with billions of genomes based on a database splitting strategy. Further, GSearch implements a three-step search strategy depending on the degree of novelty of the query genomes to maximize specificity and sensitivity. Therefore, GSearch solves a major bottleneck of microbiome studies that require genome search and/or classification.

Microbially enhanced methane uptake under warming enlarges ecosystem carbon sink in a Tibetan alpine grassland.

The alpine grasslands of the Tibetan Plateau store 23.2 Pg soil organic carbon, which becomes susceptible to microbial degradation with climate warming. However, accurate prediction of how the soil carbon stock changes under future climate warming is hampered by our limited understanding of belowground complex microbial communities. Here, we show that 4 years of warming strongly stimulated methane (CH4 ) uptake by 93.8% and aerobic respiration (CO2 ) by 11.3% in the soils of alpine grassland ecosystem. Due to no significant effects of warming on net ecosystem CO2 exchange (NEE), the warming-stimulated CH4 uptake enlarged the carbon sink capacity of whole ecosystem. Furthermore, precipitation alternation did not alter such warming effects, despite the significant effects of precipitation on NEE and soil CH4 fluxes were observed. Metagenomic sequencing revealed that warming led to significant shifts in the overall microbial community structure and the abundances of functional genes, which contrasted to no detectable changes after 2 years of warming. Carbohydrate utilization genes were significantly increased by warming, corresponding with significant increases in soil aerobic respiration. Increased methanotrophic genes and decreased methanogenic genes were observed under warming, which significantly (R2  = .59, p < .001) correlated with warming-enhanced CH4 uptakes. Furthermore, 212 metagenome-assembled genomes were recovered, including many populations involved in the degradation of various organic matter and a highly abundant methylotrophic population of the Methyloceanibacter genus. Collectively, our results provide compelling evidence that specific microbial functional traits for CH4 and CO2 cycling processes respond to climate warming with differential effects on soil greenhouse gas emissions. Alpine grasslands may play huge roles in mitigating climate warming through such microbially enhanced CH4 uptake.

Quinone Moieties Link the Microbial Respiration of Natural Organic Matter to the Chemical Reduction of Diverse Nitroaromatic Compounds.

Insensitive munitions compounds (IMCs) are emerging nitroaromatic contaminants developed by the military as safer-to-handle alternatives to conventional explosives. Biotransformation of nitroaromatics via microbial respiration has only been reported for a limited number of substrates. Important soil microorganisms can respire natural organic matter (NOM) by reducing its quinone moieties to hydroquinones. Thus, we investigated the NOM respiration combined with the abiotic reduction of nitroaromatics by the hydroquinones formed. First, we established nitroaromatic concentration ranges that were nontoxic to the quinone respiration. Then, an enrichment culture dominated by Geobacter anodireducens could indirectly reduce a broad array of nitroaromatics by first respiring NOM components or the NOM surrogate anthraquinone-2,6-disulfonate (AQDS). Without quinones, no nitroaromatic tested was reduced except for the IMC 3-nitro-1,2,4-triazol-5-one (NTO). Thus, the quinone respiration expanded the spectrum of nitroaromatics susceptible to transformation. The system functioned with very low quinone concentrations because NOM was recycled by the nitroaromatic reduction. A metatranscriptomic analysis demonstrated that the microorganisms obtained energy from quinone or NTO reduction since respiratory genes were upregulated when AQDS or NTO was the electron acceptor. The results indicated microbial NOM respiration sustained by the nitroaromatic-dependent cycling of quinones. This process can be applied as a nitroaromatic remediation strategy, provided that a quinone pool is available for microorganisms.

Microbial Functional Responses Explain Alpine Soil Carbon Fluxes under Future Climate Scenarios.

Soil microorganisms are sensitive to temperature in cold ecosystems, but it remains unclear how microbial responses are modulated by other important climate drivers, such as precipitation changes. Here, we examine the effects of six in situ warming and/or precipitation treatments in alpine grasslands on microbial communities, plants, and soil carbon fluxes. These treatments differentially affected soil carbon fluxes, gross primary production, and microbial communities. Variations of soil CO2 and CH4 fluxes across all sites significantly (r > 0.70, P < 0.050) correlated with relevant microbial functional abundances but not bacterial or fungal abundances. Given tight linkages between microbial functional traits and ecosystem functionality, we conclude that future soil carbon fluxes in alpine grasslands can be predicted by microbial carbon-degrading capacities.IMPORTANCE The warming pace in the Tibetan Plateau, which is predominantly occupied by grassland ecosystems, has been 0.2°C per decade in recent years, dwarfing the rate of global warming by a factor of 2. Many Earth system models project substantial carbon sequestration in Tibet, which has been observed. Here, we analyzed microbial communities under projected climate changes by 2100. As the soil "carbon pump," the growth and activity of microorganisms can largely influence soil carbon dynamics. However, microbial gene response to future climate scenarios is still obscure. We showed that the abundances of microbial functional genes, but not microbial taxonomy, were correlated with carbon fluxes and ecosystem multifunctionality. By identifying microbial traits linking to ecosystem functioning, our results can guide the assessment of future soil carbon fluxes in alpine grasslands, a critical step toward mitigating climate changes.

The microbial network property as a bio-indicator of antibiotic transmission in the environment.

Interspecies interaction is an essential mechanism for bacterial communities to develop antibiotic resistance via horizontal gene transfer. Nonetheless, how bacterial interactions vary along the environmental transmission of antibiotics and the underpinnings remain unclear. To address it, we explore potential microbial associations by analyzing bacterial networks generated from 16S rRNA gene sequences and functional networks containing a large number of antibiotic-resistance genes (ARGs). Antibiotic concentration decreased by more than 4000-fold along the environmental transmission chain from manure samples of swine farms to aerobic compost, compost-amended agricultural soils, and neighboring agricultural soils. Both bacterial and functional networks became larger in nodes and links with decreasing antibiotic concentrations, likely resulting from lower antibiotics stress. Nonetheless, bacterial networks became less clustered with decreasing antibiotic concentrations, while functional networks became more clustered. Modularity, a key topological property that enhances system resilience to antibiotic stress, remained high for functional networks, but the modularity values of bacterial networks were the lowest when antibiotic concentrations were intermediate. To explain it, we identified a clear shift from deterministic processes, particularly variable selection, to stochastic processes at intermediate antibiotic concentrations as the dominant mechanism in shaping bacterial communities. Collectively, our results revealed microbial network dynamics and suggest that the modularity value of association networks could serve as an important indicator of antibiotic concentrations in the environment.

Utilization of different waste proteins to create a novel PGPR-containing bio-organic fertilizer.

High-quality bio-organic fertilizers (BIOs) cannot be produced without the addition of some proteins, while many waste proteins are haphazardly disposed, causing serious environmental pollution. In this study, several waste proteins were used as additives to assist with the reproduction of the functional microbe (Bacillus amyloliquefaciens SQR9) inoculated into matured composts to produce BIOs. An optimized composition of solid-state fermentation (SSF) raw materials was predicted by response surface methodology and experimental validation. The results showed that 7.61% (w/w, DW, the same below) rapeseed meal, 8.85% expanded feather meal, 6.47% dewatered blue algal sludge and 77.07% chicken compost resulted in maximum biomass of strain SQR-9 and the maximum amount of lipopeptides 7 days after SSF. Spectroscopy experiments showed that the inner material structural changes in the novel SSF differed from the control and the novel BIO had higher dissolved organic matter. This study offers a high value-added utilization of waste proteins for producing economical but high-quality BIO.

Acute toxicity and inactivation tests of CO2 on invertebrates in drinking water treatment systems.

In addition to the esthetic problem caused by invertebrates, researchers are recently starting to be more aware of their potential importance in terms of public health. However, the inactivation methods of invertebrates which could proliferate in drinking water treatment systems are not well developed. The objective of this study is to assess the acute toxicity and inactivation effects of CO2 on familiar invertebrates in water treatment processes. The results of this study revealed that CO2 has a definite toxicity to familiar invertebrates. The values of 24-h LC50 (median lethal concentration) were calculated for each test with six groups of invertebrates. The toxicity of CO2 was higher with increasing concentrations in solution but was lower with the increase in size of the invertebrates. Above the concentration of 1,000 mg/L for the CO2 solution, the 100% inactivation time of all the invertebrates was less than 5 s, and in 15 min, the inactivation ratio showed a gradient descent with a decline in concentration. As seen for Mesocyclops thermocyclopoides, by dosing with a sodium bicarbonate solution first and adding a dilute hydrochloric acid solution 5 min later, it is possible to obtain a satisfactory inactivation effect in the GAC (granular activated carbon) filters.