Relationships Between Soil Microbial Diversities Across an Aridity Gradient in Temperate Grasslands : Soil Microbial Diversity Relationships.

Soil microbes assemble in highly complex and diverse microbial communities, and microbial diversity patterns and their drivers have been studied extensively. However, diversity correlations and co-occurrence patterns between bacterial, fungal, and archaeal domains and between microbial functional groups in arid regions remain poorly understood. Here we assessed the relationships between the diversity and abundance of bacteria, fungi, and archaea and explored how environmental factors influence these relationships. We sampled soil along a 1500-km-long aridity gradient in temperate grasslands of Inner Mongolia (China) and sequenced the 16S rRNA gene of bacteria and archaea and the ITS2 gene of fungi. The diversity correlations and co-occurrence patterns between bacterial, fungal, and archaeal domains and between different microbial functional groups were evaluated using α-diversity and co-occurrence networks based on microbial abundance. Our results indicate insignificant correlations among the diversity patterns of bacterial, fungal, and archaeal domains using α-diversity but mostly positive correlations among diversity patterns of microbial functional groups based on α-diversity and co-occurrence networks along the aridity gradient. These results suggest that studying microbial diversity patterns from the perspective of functional groups and co-occurrence networks can provide additional insights on patterns that cannot be accessed using only overall microbial α-diversity. Increase in aridity weakens the diversity correlations between bacteria and fungi and between bacterial and archaeal functional groups, but strengthens the positive diversity correlations between bacterial functional groups and between fungal functional groups and the negative diversity correlations between bacterial and fungal functional groups. These variations of the diversity correlations are associated with the different responses of microbes to environmental factors, especially aridity. Our findings demonstrate the complex responses of microbial community structure to environmental conditions (especially aridity) and suggest that understanding diversity correlations and co-occurrence patterns between soil microbial groups is essential for predicting changes in microbial communities under future climate change in arid regions.

Carbon pools in China's terrestrial ecosystems: New estimates based on an intensive field survey.

China's terrestrial ecosystems have functioned as important carbon sinks. However, previous estimates of carbon budgets have included large uncertainties owing to the limitations of sample size, multiple data sources, and inconsistent methodologies. In this study, we conducted an intensive field campaign involving 14,371 field plots to investigate all sectors of carbon stocks in China's forests, shrublands, grasslands, and croplands to better estimate the regional and national carbon pools and to explore the biogeographical patterns and potential drivers of these pools. The total carbon pool in these four ecosystems was 79.24 ± 2.42 Pg C, of which 82.9% was stored in soil (to a depth of 1 m), 16.5% in biomass, and 0.60% in litter. Forests, shrublands, grasslands, and croplands contained 30.83 ± 1.57 Pg C, 6.69 ± 0.32 Pg C, 25.40 ± 1.49 Pg C, and 16.32 ± 0.41 Pg C, respectively. When all terrestrial ecosystems are taken into account, the country's total carbon pool is 89.27 ± 1.05 Pg C. The carbon density of the forests, shrublands, and grasslands exhibited a strong correlation with climate: it decreased with increasing temperature but increased with increasing precipitation. Our analysis also suggests a significant sequestration potential of 1.9-3.4 Pg C in forest biomass in the next 10-20 years assuming no removals, mainly because of forest growth. Our results update the estimates of carbon pools in China's terrestrial ecosystems based on direct field measurements, and these estimates are essential to the validation and parameterization of carbon models in China and globally.

Patterns of plant carbon, nitrogen, and phosphorus concentration in relation to productivity in China's terrestrial ecosystems.

Plant nitrogen (N) and phosphorus (P) content regulate productivity and carbon (C) sequestration in terrestrial ecosystems. Estimates of the allocation of N and P content in plant tissues and the relationship between nutrient content and photosynthetic capacity are critical to predicting future ecosystem C sequestration under global change. In this study, by investigating the nutrient concentrations of plant leaves, stems, and roots across China's terrestrial biomes, we document large-scale patterns of community-level concentrations of C, N, and P. We also examine the possible correlation between nutrient content and plant production as indicated by vegetation gross primary productivity (GPP). The nationally averaged community concentrations of C, N, and P were 436.8, 14.14, and 1.11 mg·g-1 for leaves; 448.3, 3.04 and 0.31 mg·g-1 for stems; and 418.2, 4.85, and 0.47 mg·g-1 for roots, respectively. The nationally averaged leaf N and P productivity was 249.5 g C GPP·g-1 N·y-1 and 3,157.9 g C GPP·g-1 P·y-1, respectively. The N and P concentrations in stems and roots were generally more sensitive to the abiotic environment than those in leaves. There were strong power-law relationships between N (or P) content in different tissues for all biomes, which were closely coupled with vegetation GPP. These findings not only provide key parameters to develop empirical models to scale the responses of plants to global change from a single tissue to the whole community but also offer large-scale evidence of biome-dependent regulation of C sequestration by nutrients.

Effects of national ecological restoration projects on carbon sequestration in China from 2001 to 2010.

The long-term stressful utilization of forests and grasslands has led to ecosystem degradation and C loss. Since the late 1970s China has launched six key national ecological restoration projects to protect its environment and restore degraded ecosystems. Here, we conducted a large-scale field investigation and a literature survey of biomass and soil C in China's forest, shrubland, and grassland ecosystems across the regions where the six projects were implemented (∼16% of the country's land area). We investigated the changes in the C stocks of these ecosystems to evaluate the contributions of the projects to the country's C sink between 2001 and 2010. Over this decade, we estimated that the total annual C sink in the project region was 132 Tg C per y (1 Tg = 1012 g), over half of which (74 Tg C per y, 56%) was attributed to the implementation of the projects. Our results demonstrate that these restoration projects have substantially contributed to CO2 mitigation in China.

Rapid loss of lakes on the Mongolian Plateau.

Lakes are widely distributed on the Mongolian Plateau and, as critical water sources, have sustained Mongolian pastures for hundreds of years. However, the plateau has experienced significant lake shrinkage and grassland degradation during the past several decades. To quantify the changes in all of the lakes on the plateau and the associated driving factors, we performed a satellite-based survey using multitemporal Landsat images from the 1970s to 2000s, combined with ground-based censuses. Our results document a rapid loss of lakes on the plateau in the past decades: the number of lakes with a water surface area >1 km(2) decreased from 785 in the late 1980s to 577 in 2010, with a greater rate of decrease (34.0%) in Inner Mongolia of China than in Mongolia (17.6%). This decrease has been particularly pronounced since the late 1990s in Inner Mongolia and the number of lakes >10 km(2) has declined by 30.0%. The statistical analyses suggested that in Mongolia precipitation was the dominant driver for the lake changes, and in Inner Mongolia coal mining was most important in its grassland area and irrigation was the leading factor in its cultivated area. The deterioration of lakes is expected to continue in the following decades not only because of changing climate but also increasing exploitation of underground mineral and groundwater resources on the plateau. To protect grasslands and the indigenous nomads, effective action is urgently required to save these valuable lakes from further deterioration.

Vegetation carbon sequestration in Chinese forests from 2010 to 2050.

Forests store a large part of the terrestrial vegetation carbon (C) and have high C sequestration potential. Here, we developed a new forest C sequestration (FCS) model based on the secondary succession theory, to estimate vegetation C sequestration capacity in China's forest vegetation. The model used the field measurement data of 3161 forest plots and three future climate scenarios. The results showed that logistic equations provided a good fit for vegetation biomass with forest age in natural and planted forests. The FCS model has been verified with forest biomass data, and model uncertainty is discussed. The increment of vegetation C storage in China's forest vegetation from 2010 to 2050 was estimated as 13.92 Pg C, while the average vegetation C sequestration rate was 0.34 Pg C yr-1 with a 95% confidence interval of 0.28-0.42 Pg C yr-1 , which differed significantly between forest types. The largest contributor to the increment was deciduous broadleaf forest (37.8%), while the smallest was deciduous needleleaf forest (2.7%). The vegetation C sequestration rate might reach its maximum around 2020, although vegetation C storage increases continually. It is estimated that vegetation C sequestration might offset 6-8% of China's future emissions. Furthermore, there was a significant negative relationship between vegetation C sequestration rate and C emission rate in different provinces of China, suggesting that developed provinces might need to compensate for undeveloped provinces through C trade. Our findings will provide valuable guidelines to policymakers for designing afforestation strategies and forest C trade in China.

Evidence for environmentally enhanced forest growth.

Forests in the middle and high latitudes of the northern hemisphere function as a significant sink for atmospheric carbon dioxide (CO2). This carbon (C) sink has been attributed to two processes: age-related growth after land use change and growth enhancement due to environmental changes, such as elevated CO2, nitrogen deposition, and climate change. However, attribution between these two processes is largely controversial. Here, using a unique time series of an age-class dataset from six national forest inventories in Japan and a new approach developed in this study (i.e., examining changes in biomass density at each age class over the inventory periods), we quantify the growth enhancement due to environmental changes and its contribution to biomass C sink in Japan's forests. We show that the growth enhancement for four major plantations was 4.0∼7.7 Mg C⋅ha(-1) from 1980 to 2005, being 8.4-21.6% of biomass C sequestration per hectare and 4.1-35.5% of the country's total net biomass increase of each forest type. The growth enhancement differs among forest types, age classes, and regions. Our results provide, to our knowledge, the first ground-based evidence that global environmental changes can increase C sequestration in forests on a broad geographic scale and imply that both the traits and age of trees regulate the responses of forest growth to environmental changes. These findings should be incorporated into the prediction of forest C cycling under a changing climate.

Forest biomass carbon sinks in East Asia, with special reference to the relative contributions of forest expansion and forest growth.

Forests play an important role in regional and global carbon (C) cycles. With extensive afforestation and reforestation efforts over the last several decades, forests in East Asia have largely expanded, but the dynamics of their C stocks have not been fully assessed. We estimated biomass C stocks of the forests in all five East Asian countries (China, Japan, North Korea, South Korea, and Mongolia) between the 1970s and the 2000s, using the biomass expansion factor method and forest inventory data. Forest area and biomass C density in the whole region increased from 179.78 × 10(6) ha and 38.6 Mg C ha(-1) in the 1970s to 196.65 × 10(6) ha and 45.5 Mg C ha(-1) in the 2000s, respectively. The C stock increased from 6.9 Pg C to 8.9 Pg C, with an averaged sequestration rate of 66.9 Tg C yr(-1). Among the five countries, China and Japan were two major contributors to the total region's forest C sink, with respective contributions of 71.1% and 32.9%. In China, the areal expansion of forest land was a larger contributor to C sinks than increased biomass density for all forests (60.0% vs. 40.0%) and for planted forests (58.1% vs. 41.9%), while the latter contributed more than the former for natural forests (87.0% vs. 13.0%). In Japan, increased biomass density dominated the C sink for all (101.5%), planted (91.1%), and natural (123.8%) forests. Forests in South Korea also acted as a C sink, contributing 9.4% of the total region's sink because of increased forest growth (98.6%). Compared to these countries, the reduction in forest land in both North Korea and Mongolia caused a C loss at an average rate of 9.0 Tg C yr(-1), equal to 13.4% of the total region's C sink. Over the last four decades, the biomass C sequestration by East Asia's forests offset 5.8% of its contemporary fossil-fuel CO2 emissions.

Artificial light at night causes community instability of bacterial community in urban soils.

Urban soils host diverse bacteria crucial for ecosystem functions and urban health. As urbanization rises, artificial light at night (ALAN) imposes disturbances on soil ecosystems, yet how ALAN affects the structure and stability of soil bacterial community remains unclear. Here we coupled a short-term incubation experiment, community profiling, network analysis, and in situ field survey to assess the ecological impacts of ALAN. We showed that ALAN influenced bacterial compositions and shifted the bacterial network to a less stable phase, altering denitrification potential. Such transition in community stability probably resulted from an ALAN-induced decrease in competition and/or an increase in facilitation, in line with the Stress Gradient Hypothesis. Similar destabilizing effects were also detected in bacterial networks in multiple urban soils subjected to different levels of ALAN stress, supporting the action of ALAN on naturally-occurring soil bacterial communities. Overall, our findings highlight ALAN as a new form of anthropogenic stress that jeopardizes the stability of soil bacterial community, which would facilitate ecological projection of expanding ALAN exposure.

Global abundance patterns, diversity, and ecology of Patescibacteria in wastewater treatment plants.

BACKGROUND: Microorganisms are responsible for nutrient removal and resource recovery in wastewater treatment plants (WWTPs), and their diversity is often studied by 16S rRNA gene amplicon sequencing. However, this approach underestimates the abundance and diversity of Patescibacteria due to the low coverage of commonly used PCR primers for this highly divergent bacterial phylum. Therefore, our current understanding of the global diversity, distribution, and ecological role of Patescibacteria in WWTPs is very incomplete. This is particularly relevant as Patescibacteria are considered to be associated with microbial host cells and can therefore influence the abundance and temporal variability of other microbial groups that are important for WWTP functioning. RESULTS: Here, we evaluated the in silico coverage of widely used 16S rRNA gene-targeted primer pairs and redesigned a primer pair targeting the V4 region of bacterial and archaeal 16S rRNA genes to expand its coverage for Patescibacteria. We then experimentally evaluated and compared the performance of the original and modified V4-targeted primers on 565 WWTP samples from the MiDAS global sample collection. Using the modified primer pair, the percentage of ASVs classified as Patescibacteria increased from 5.9 to 23.8%, and the number of detected patescibacterial genera increased from 560 to 1576, while the detected diversity of the remaining microbial community remained similar. Due to this significantly improved coverage of Patescibacteria, we identified 23 core genera of Patescibacteria in WWTPs and described the global distribution pattern of these unusual microbes in these systems. Finally, correlation network analysis revealed potential host organisms that might be associated with Patescibacteria in WWTPs. Interestingly, strong indications were found for an association between Patescibacteria of the Saccharimonadia and globally abundant polyphosphate-accumulating organisms of the genus Ca. Phosphoribacter. CONCLUSIONS: Our study (i) provides an improved 16S rRNA gene V4 region-targeted amplicon primer pair inclusive of Patescibacteria with little impact on the detection of other taxa, (ii) reveals the diversity and distribution patterns of Patescibacteria in WWTPs on a global scale, and (iii) provides new insights into the ecological role and potential hosts of Patescibacteria in WWTPs. Video Abstract.

Population structure and antibiotic resistance of swine extraintestinal pathogenic Escherichia coli from China.

Extraintestinal Pathogenic Escherichia coli (ExPEC) pose a significant threat to human and animal health. However, the diversity and antibiotic resistance of animal ExPEC, and their connection to human infections, remain largely unexplored. The study performs large-scale genome sequencing and antibiotic resistance testing of 499 swine-derived ExPEC isolates from China. Results show swine ExPEC are phylogenetically diverse, with over 80% belonging to phylogroups B1 and A. Importantly, 15 swine ExPEC isolates exhibit genetic relatedness to human-origin E. coli strains. Additionally, 49 strains harbor toxins typical of enteric E. coli pathotypes, implying hybrid pathotypes. Notably, 97% of the total strains are multidrug resistant, including resistance to critical human drugs like third- and fourth-generation cephalosporins. Correspondingly, genomic analysis unveils prevalent antibiotic resistance genes (ARGs), often associated with co-transfer mechanisms. Furthermore, analysis of 20 complete genomes illuminates the transmission pathways of ARGs within swine ExPEC and to human pathogens. For example, the transmission of plasmids co-harboring fosA3, blaCTX-M-14, and mcr-1 genes between swine ExPEC and human-origin Salmonella enterica is observed. These findings underscore the importance of monitoring and controlling ExPEC infections in animals, as they can serve as a reservoir of ARGs with the potential to affect human health or even be the origin of pathogens infecting humans.

Population genomics and pathotypic evaluation of the bacterial leaf blight pathogen of rice reveals rapid evolutionary dynamics of a plant pathogen.

The Xanthomonas oryzae pv. oryzae (Xoo) is a bacterial pathogen causing bacterial blight disease in rice, resulting in significant yield reductions of up to 50% in rice production. Despite its serious threat to food production globally, knowledge of its population structure and virulence evolution is relatively limited. In this study, we employed whole-genome sequencing to explore the diversity and evolution of Xoo in the main rice-growing areas of China over the past 30 years. Using phylogenomic analysis, we revealed six lineages. CX-1 and CX-2 primarily contained Xoo isolates from South China, while CX-3 represented Xoo isolates from North China. Xoo isolates belonging to CX-5 and CX-6 were the most prevalent across all studied areas, persisting as dominant lineages for several decades. Recent sporadic disease outbreaks were primarily caused by Xoo isolates derived from the two major lineages, CX-5 and CX-6, although Xoo isolates from other lineages also contributed to these outbreaks. The lineage and sub-lineage distributions of Xoo isolates were strongly correlated with their geographical origin, which was found to be mainly determined by the planting of the two major rice subspecies, indica and japonica. Moreover, large-scale virulence testing was conducted to evaluate the diversity of pathogenicity for Xoo. We found rapid virulence evolution against rice, and its determinant factors included the genetic background of Xoo, rice resistance genes, and planting environment of rice. This study provides an excellent model for understanding the evolution and dynamics of plant pathogens in the context of their interactions with their hosts, which are shaped by a combination of geographical conditions and farming practices. The findings of this study may have important implications for the development of effective strategies for disease management and crop protection in rice production systems.

Accounting carbon storage in decaying root systems of harvested forests.

Decaying root systems of harvested trees can be a significant component of belowground carbon storage, especially in intensively managed forests where harvest occurs repeatedly in relatively short rotations. Based on destructive sampling of root systems of harvested loblolly pine trees, we estimated that root systems contained about 32% (17.2 Mg ha(-1)) at the time of harvest, and about 13% (6.1 Mg ha(-1)) of the soil organic carbon 10 years later. Based on the published roundwood output data, we estimated belowground biomass at the time of harvest for loblolly-shortleaf pine forests harvested between 1995 and 2005 in South Carolina. We then calculated C that remained in the decomposing root systems in 2005 using the decay function developed for loblolly pine. Our calculations indicate that the amount of C stored in decaying roots of loblolly-shortleaf pine forests harvested between 1995 and 2005 in South Carolina was 7.1 Tg. Using a simple extrapolation method, we estimated 331.8 Tg C stored in the decomposing roots due to timber harvest from 1995 to 2005 in the conterminous USA. To fully account for the C stored in the decomposing roots of the US forests, future studies need (1) to quantify decay rates of coarse roots for major tree species in different regions, and (2) to develop a methodology that can determine C stock in decomposing roots resulting from natural mortality.

Yield and quality properties of silage maize and their influencing factors in China.

Silage maize (Zea mays L.) is one of the most important forages in the world, and its yield and quality properties are critical parameters for livestock production and assessment of forage values. However, relationships between its yield and quality properties and the controlling factors are not well documented. In this study, we collected 5,663 observations from 196 publications across the country to identify the relationships between yield and quality properties of silage maize and to assess the impact of management practices and climatic factors on its yield and quality in China. The average dry matter yield of silage maize was (19.98±6.93) Mg ha-1, and the average value of crude protein, ether extract, crude ash, crude fiber, acid detergent fiber, neutral detergent fiber, nitrogen-free extract, and relative feed value was 7.86%±1.71%, 2.53%±1.01%, 5.05%±1.66%, 23.97%±6.34%, 27.62%±7.12%, 51.60%±9.85%, 59.68%±7.72%, and 131.17±31.49, respectively. In general, its nutritive value decreased as its yield increased. Increasing planting density could increase the yield but inhibit the nutritive values, while increasing fertilization could benefit the nutritive values. Geographically, the yield increased and the nutritive value decreased from warm (south) to cold (north) regions. The length of growth duration was a major controlling factor for the patterns of these properties. Our findings provide insights for police-makers to make strategy for achieving high yield and good quality of silage maize and help local people to implement better management practices.

Terrestrial carbon sinks in China and around the world and their contribution to carbon neutrality.

Enhancing the terrestrial ecosystem carbon sink (referred to as terrestrial C sink) is an important way to slow down the continuous increase in atmospheric carbon dioxide (CO2) concentration and to achieve carbon neutrality target. To better understand the characteristics of terrestrial C sinks and their contribution to carbon neutrality, this review summarizes major progress in terrestrial C budget researches during the past decades, clarifies spatial patterns and drivers of terrestrial C sources and sinks in China and around the world, and examines the role of terrestrial C sinks in achieving carbon neutrality target. According to recent studies, the global terrestrial C sink has been increasing from a source of (-0.2±0.9) Pg C yr-1 (1 Pg=1015 g) in the 1960s to a sink of (1.9±1.1) Pg C yr-1 in the 2010s. By synthesizing the published data, we estimate terrestrial C sink of 0.20-0.25 Pg C yr-1 in China during the past decades, and predict it to be 0.15-0.52 Pg C yr-1 by 2060. The terrestrial C sinks are mainly located in the mid- and high latitudes of the Northern Hemisphere, while tropical regions act as a weak C sink or source. The C balance differs much among ecosystem types: forest is the major C sink; shrubland, wetland and farmland soil act as C sinks; and whether the grassland functions as C sink or source remains unclear. Desert might be a C sink, but the magnitude and the associated mechanisms are still controversial. Elevated atmospheric CO2 concentration, nitrogen deposition, climate change, and land cover change are the main drivers of terrestrial C sinks, while other factors such as fires and aerosols would also affect ecosystem C balance. The driving factors of terrestrial C sink differ among regions. Elevated CO2 concentration and climate change are major drivers of the C sinks in North America and Europe, while afforestation and ecological restoration are additionally important forcing factors of terrestrial C sinks in China. For future studies, we recommend the necessity for intensive and long term ecosystem C monitoring over broad geographic scale to improve terrestrial biosphere models for accurately evaluating terrestrial C budget and its dynamics under various climate change and policy scenarios.

Elucidation of the Pathogenicity-Associated Regulatory Network in Xanthomonas oryzae pv. oryzae.

Xanthomonas is a notorious plant pathogen causing serious diseases in hundreds of plant hosts. Xanthomonas species are equipped with an array of signal transduction systems that regulate gene expression to survive in various harsh environments and successfully infect hosts. Although certain pathogenicity-associated regulators have been functionally characterized, signal transduction systems always function as a regulatory network which remains to be elucidated in Xanthomonas This study used a systematic approach to characterize all identified pathogenicity-associated regulators in Xanthomonas oryzae pv. oryzae (Xoo), including a transcriptional regulator with unknown function, and their interactive regulatory network. RNA sequencing was used in elucidating the patterns of the 10 pathogenicity-associated regulators identified. Results revealed that each pathogenicity-associated regulator has cross talk with others and all these regulators function as a regulatory network, with VemR and PXO_RS20790 being the master pathogenicity-associated regulators and HrpX being the final executant. Moreover, regulome analysis showed that numerous genes other than genes in pathogenicity islands are finely regulated within the regulatory network. Given that most of the pathogenicity-associated regulators are conserved in Xanthomonadales, our findings suggest a global network of gene regulation in this evolutionarily conserved pathogen. In conclusion, our study provides essential basic information about the regulatory network in Xoo, suggesting that this complicated regulatory network is one of the reasons for the robustness and fitness of Xanthomonas spp.IMPORTANCE The host plant infection process of pathogenic bacteria is a coordinating cellular behavior, which requires dynamic regulation at several levels in response to variations in host plants or fluctuations in the external environment. As one of the most important genera of plant-pathogenic bacteria, Xanthomonas has been studied as a model. Although certain pathogenicity-associated regulators have been functionally characterized, interactions among them remain to be elucidated. This study systematically characterized pathogenicity-associated regulators in Xoo and revealed that cross talk exists among pathogenicity-associated regulators and function as a regulatory network in which a hierarchy exists among the regulators. Our study elucidated the landscape of the pathogenicity-associated regulatory network in Xanthomonas, promoting understanding of the infection process of pathogenic bacteria.

Ecology and Function of the Transmissible Locus of Stress Tolerance in Escherichia coli and Plant-Associated Enterobacteriaceae.

The transmissible locus of stress tolerance (tLST) is a genomic island which confers resistance to heat and chlorine. In this study, we determined that the tLST is frequent in genomes of those Enterobacteriaceae that occur in association with plants as well as the intestines of humans and animals and are relevant as nosocomial pathogens, e.g., Klebsiella and Cronobacter species. The tLST is more frequent in environmental and clinical isolates of Klebsiella pneumoniae than in animal isolates, and heat and chlorine resistance of tLST-positive strains of K. pneumoniae matched the resistance of tLST-positive strains of Escherichia coli. The function of 13 tLST genes was determined by assessing the heat and chlorine resistance of E. coli MG1655 mutants. The deletion of sHsp20, clpKGI, sHspGI, pscA, pscB, and hdeDGI reduced both heat and chlorine resistance; deletion of kefB reduced only chlorine resistance. Genes coding for heat shock proteins sHsp20, clpKGI, and sHspGI decreased the oxidation of cytoplasmic proteins, while kefB decreased the oxidation of membrane lipids. The fitness cost of the tLST for E. coli MG1655 was assessed by pairwise competition experiments with isogenic tLST-positive or tLST-negative strains. The tLST imposes a fitness cost that is compensated for by frequent and lethal challenges with chlorine. All core genes need to be present to maintain the ecological advantage relative to the fitness cost. Taken together, core tLST genes are necessary to provide protection for E. coli against heat and chlorine stress, and the selective pressure for the tLST maintains core genes. IMPORTANCE The transmissible locus of stress tolerance (tLST) is a genomic island comprising 10 core genes that occurs in diverse Enterobacteriaceae and confers resistance to heat and chlorine. Experimentation described in the manuscript describes the physiological function of the core genes by characterization of the resistance of 13 single-knockout (KO) mutants and by characterization of protein and membrane oxidation in these strains after chlorine challenge. Results identify tLST resistance as a genomic island that is specific for those Enterobacteriaceae that occur in plant-associated habitats as well in the intestines of vertebrates. In addition, the ecological function of the genomic island was characterized by large-scale genomic analysis and competition experiments of wild-type and mutant strains. Results suggest that tLST-mediated resistance to chlorine may contribute to the persistence of nosocomial pathogens in hospitals.

Relative Importance of Deterministic and Stochastic Processes on Soil Microbial Community Assembly in Temperate Grasslands.

Changes in species composition across communities, i.e., ß-diversity, is a central focus of ecology. Compared to macroorganisms, the ß-diversity of soil microbes and its drivers are less studied. Whether the determinants of soil microbial ß-diversity are consistent between soil depths and between abundant and rare microorganisms remains controversial. Here, using the 16S-rRNA of soil bacteria and archaea sampled at different soil depths (0-10 and 30-50 cm) from 32 sites along an aridity gradient of 1500 km in the temperate grasslands in northern China, we compared the effects of deterministic and stochastic processes on the taxonomic and phylogenetic ß-diversity of soil microbes. Using variation partitioning and null models, we found that the taxonomic ß-diversity of the overall bacterial communities was more strongly determined by deterministic processes in both soil layers (the explanatory power of environmental distance in topsoil: 25.4%; subsoil: 47.4%), while their phylogenetic counterpart was more strongly determined by stochastic processes (the explanatory power of spatial distance in topsoil: 42.1; subsoil 24.7%). However, in terms of abundance, both the taxonomic and phylogenetic ß-diversity of the abundant bacteria in both soil layers was more strongly determined by deterministic processes, while those of rare bacteria were more strongly determined by stochastic processes. In comparison with bacteria, both the taxonomic and phylogenetic ß-diversity of the overall abundant and rare archaea were strongly determined by deterministic processes. Among the variables representing deterministic processes, contemporary and historical climate and aboveground vegetation dominated the microbial ß-diversity of the overall and abundant microbes of both domains in topsoils, but soil geochemistry dominated in subsoils. This study presents a comprehensive understanding on the ß-diversity of soil microbial communities in the temperate grasslands in northern China. Our findings highlight the importance of soil depth, phylogenetic turnover, and species abundance in the assembly processes of soil microbial communities.

Metagenomic reconstructions of gut microbial metabolism in weanling pigs.

BACKGROUND: The piglets' transition from milk to solid feed induces a succession of bacterial communities, enhancing the hosts' ability to harvest energy from dietary carbohydrates. To reconstruct microbial carbohydrate metabolism in weanling pigs, this study combined 16S rRNA gene sequencing (n = 191) and shotgun metagenomics (n = 72). RESULTS: Time and wheat content in feed explained most of the variation of the microbiota as assessed by 16S rRNA gene sequencing in weanling pigs. De novo metagenomic binning reconstructed 360 high-quality genomes that represented 11 prokaryotic and 1 archaeal phylum. Analysis of carbohydrate metabolism in these genomes revealed that starch fermentation is carried out by a consortium of Firmicutes expressing extracellular α-(1 → 4)-glucan branching enzyme (GH13) and Bacteroidetes expressing periplasmic neopullulanase (GH13) and α-glucosidase (GH97). Fructans were degraded by extracellular GH32 enzymes from Bacteriodetes and Lactobacillus. Lactose fermentation by ß-galactosidases (GH2 and GH42) was identified in Firmicutes. In conclusion, the assembly of 360 high-quality genomes as the first metagenomic reference for swine intestinal microbiota allowed identification of key microbial contributors to degradation of starch, fructans, and lactose. CONCLUSIONS: Microbial consortia that are responsible for degradation of these glycans differ substantially from the microbial consortia that degrade the same glycans in humans. Our study thus enables improvement of feeding models with higher feed efficiency and better pathogen control for weanling pigs.

Contrasting Biogeographic Patterns of Bacterial and Archaeal Diversity in the Top- and Subsoils of Temperate Grasslands.

Biogeographic patterns and drivers of soil microbial diversity have been extensively studied in the past few decades. However, most research has focused on the topsoil, while the subsoil is assumed to have microbial diversity patterns similar to those of the topsoil. Here we compared patterns and drivers of microbial alpha and beta diversity in and between topsoils (0 to 10 cm) and subsoils (30 to 50 cm) of temperate grasslands in Inner Mongolia of China, covering an ∼1,500-km transect along an aridity gradient. Counter to the conventional assumption, we find contrasting biogeographic patterns of diversity and influencing factors for different bacterial and archaeal groups and between depths. While bacterial diversity remains constant or increases with increasing aridity in topsoil and decreases in subsoil, archaeal diversity decreases in topsoil and remains constant in subsoil. Microbial diversity in the topsoil is most strongly influenced by aboveground vegetation and contemporary climate but is most strongly influenced by the factor historical temperature anomaly since the Last Glacial Maximum (LGM) and by soil pH in the subsoil. Moreover, the biogeographic patterns of topsoil-subsoil community dissimilarities vary for different microbial groups and are overall most strongly influenced by soil fertility differences between depths for bacteria and by contemporary climate for archaea. These findings suggest that diversity patterns observed in the topsoil may not be readily applied to the subsoil horizons. For the subsoil in particular, historical climate plays a vital role in the spatial variation of bacterial diversity. Overall, our study provides novel information for understanding and predicting soil microbial diversity patterns at depth.IMPORTANCE Exploring the biogeographic patterns of soil microbial diversity is critical for understanding mechanisms underlying the response of soil processes to climate change. Using top- and subsoils from an ∼1,500-km temperate grassland transect, we find divergent patterns of microbial diversity and its determinants in the topsoil versus the subsoil. Furthermore, we find important and direct legacy effects of historical climate change on the microbial diversity of subsoil yet indirect effects on topsoil. Our findings challenge the conventional assumption of similar geographic patterns of soil microbial diversity along soil profiles and help to improve our understanding of how soil microbial communities may respond to future climate change in different regions with various climate histories.