Diurnal Temperature Variation and Plants Drive Latitudinal Patterns in Seasonal Dynamics of Soil Microbial Community

Seasonal variations in soil microbial community co-occurrence network complexity respond differently to field-simulated warming experiments in a northern subtropical forest

Global warming may reshape seasonal changes in microbial community diversity and co-occurrence network patterns, with significant implications for terrestrial ecosystem function. We conducted a 2-year in situ field simulation of the effects of warming on the seasonal dynamics of soil microbial communities in a northern subtropical Quercus acutissima forest. Our study revealed that warming had no significant effect on the richness or diversity of soil bacteria or fungi in the growing season, whereas different warming gradients had different effects on their diversity in the nongrowing season. Warming also changed the microbial community structure, increasing the abundance of some thermophilic microbial species and decreasing the abundance of some symbiotrophic microorganisms. The co-occurrence network analysis of the microbial community showed that warming decreased the complexity of the intradomain network in the soil bacterial community in the growing and nongrowing seasons but increased it in the fungal community. Moreover, increasing warming temperatures increased the complexity of the interdomain network between bacteria and fungi in the growing season but decreased it in the nongrowing season, and the keystone species in the interdomain network changed with warming. Warming also reduced the proportion of positive microbial community interactions, indicating that warming reduced the mutualism, commensalism, and neutralism of microorganisms as they adapted to soil environmental stress. The factors affecting the fungal community varied considerably across warming gradients, with the bacterial community being significantly affected by soil temperature, MBC, NO3--N and NH4+-N, moreover, SOC and TN significantly affected fungal communities in the 4 °C warming treatment. These results suggest that warming increases seasonal differences in the diversity and complexity of soil microbial communities in the northern subtropical region, significantly influencing soil dynamic processes regulating forest ecosystems under global warming.

Anatomy of a mega-radiation: Biogeography and niche evolution in Astragalus

PREMISE

Astragalus (Fabaceae), with more than 3000 species, represents a globally successful radiation of morphologically highly similar species predominant across the northern hemisphere. It has attracted attention from systematists and biogeographers, who have asked what factors might be behind the extraordinary diversity of this important arid-adapted clade and what sets it apart from close relatives with far less species richness.

METHODS

Here, for the first time using extensive phylogenetic sampling, we asked whether (1) Astragalus is uniquely characterized by bursts of radiation or whether diversification instead is uniform and no different from closely related taxa. Then we tested whether the species diversity of Astragalus is attributable specifically to its predilection for (2) cold and arid habitats, (3) particular soils, or to (4) chromosome evolution. Finally, we tested (5) whether Astragalus originated in central Asia as proposed and (6) whether niche evolutionary shifts were subsequently associated with the colonization of other continents.

RESULTS

Our results point to the importance of heterogeneity in the diversification of Astragalus, with upshifts associated with the earliest divergences but not strongly tied to any abiotic factor or biogeographic regionalization tested here. The only potential correlate with diversification we identified was chromosome number. Biogeographic shifts have a strong association with the abiotic environment and highlight the importance of central Asia as a biogeographic gateway.

CONCLUSIONS

Our investigation shows the importance of phylogenetic and evolutionary studies of logistically challenging "mega-radiations." Our findings reject any simple key innovation behind high diversity and underline the often nuanced, multifactorial processes leading to species-rich clades.

The Relationship between Endophytic Fungi of Chimonanthus praecox and Volatile Metabolites under Different Circadian Rhythms and Blooming Stages

Chimonanthus praecox is an aromatic plant that flowers in winter. The composition of the floral volatiles of C. praecox is influenced by different blooming stages, circadian rhythms and species. However, the relationship between floral volatiles and plant endophytic fungi has not received much research attention. Here, we used high-throughput sequencing technology to compare and analyze the changes in the structure and diversity of the endophytic fungal communities in C. praecox under different circadian rhythms (7:00 a.m., 1:00 p.m., and 7:00 p.m.) and in different blooming stages (unopened flowers and opened flowers). The endophytic fungi of C. praecox consisted of nine phyla, 34 classes, 79 orders, 181 families, 293 genera, and 397 species, and Ascomycota was the dominant phylum. Under a diurnal rhythm, the diversity (Chao1 and Shannon indices) of endophytic fungi gradually decreased in the unopened flowers, while an increasing and then decreasing trend was found for the opened flowers. In the different blooming stages, the endophytic fungal diversity was significantly higher at 7:00 a.m. in the unopened flowers compared to the opened flowers. Humidity was the key factors that significantly affected the endophytic fungal diversity and community. Moreover, 11 endophytic fungi were significantly positively or negatively correlated with seven floral volatiles. In conclusion, the community structure and diversity of endophytic fungi in C. praecox were affected by the different blooming stages and circadian rhythms, and a correlation effect related to floral volatiles was found, but there are other possible reasons that were not tested. This study provides a theoretical basis for elucidating the interrelationships between endophytic fungi, floral volatiles, and environmental factors in C. praecox.

Review: Research progress on seasonal succession of phyllosphere microorganisms

Phyllosphere microorganisms have recently attracted the attention of scientists studying plant microbiomes. The origin, diversity, functions, and interactions of phyllosphere microorganisms have been extensively explored. Many experiments have demonstrated seasonal cycles of phyllosphere microbes. However, a comprehensive comparison of these separate investigations to characterize seasonal trends in phyllosphere microbes of woody and herbaceous plants has not been conducted. In this review, we explored the dynamic changes of phyllosphere microorganisms in woody and non-woody plants with the passage of the season, sought to find the driving factors, summarized these texts, and thought about future research trends regarding the application of phyllosphere microorganisms in agricultural production. Seasonal trends in phyllosphere microorganisms of herbaceous and woody plants have similarities and differences, but extensive experimental validation is needed. Climate, insects, hosts, microbial interactions, and anthropogenic activities are the diverse factors that influence seasonal variation in phyllosphere microorganisms.

Distribution patterns and community assembly processes of eukaryotic microorganisms along an altitudinal gradient in the middle reaches of the Yarlung Zangbo River

Eukaryotic microorganisms play an important role in the biogeochemical cycles of rivers. Dynamic hydrological processes in rivers are thought to influence the assembly processes of eukaryotic microbes, as well as affecting local geomorphology. These processes have not been extensively studied for eukaryotic river microbes in extreme environments on the Tibetan Plateau. This study used 18S rDNA gene amplification sequencing, a neutral community model, and a null model to analyze the spatial and temporal dynamics and assembly processes of eukaryotic microbial communities in the middle reaches of the Yarlung Zangbo River. We conducted analyses across wet and dry seasons, as well as varying altitudinal gradients. Our results showed that the diversity, structure, and taxonomic composition of eukaryotic microbial communities varied more with altitude than season, and the diversity of the communities first increased, then decreased, with increasing elevation. Distance-decay analysis showed that the correlation between eukaryotic microbial communities and environmental distance was stronger than the correlation between the microbial communities and geographical distance. Deterministic processes (homogeneous selection) dominated the construction of eukaryotic microbial communities, and water temperature, pH, and total phosphorus were the primary environmental factors that influenced the construction of eukaryotic microbial communities. These results expand our understanding of the characteristics of eukaryotic microbial communities in rivers on the Tibetan Plateau and provide clues to understanding the mechanisms that maintain eukaryotic microbial diversity in extreme environments.

Linking Microbial Population Succession and DOM Molecular Changes in Synechococcus-Derived Organic Matter Addition Incubation

The molecular-level interactions between phytoplankton-derived dissolved organic matter (DOM) and heterotrophic prokaryotes represent a fundamental and yet poorly understood component of the marine elemental cycle. Here, we investigated the degradation of Synechococcus-derived organic matter (SynOM) by coastal microorganisms using spectroscopic and ultrahigh-resolution mass spectrometry analyses coupled with high-throughput sequencing. The added SynOM showed a spectrum of reactivity during a 180-day dark incubation experiment. Along with the decrease in DOM bioavailability, the chemical properties of DOM molecules overall showed increases in oxidation state and aromaticity. Both the microbial community and DOM molecular compositions became more homogeneous toward the end of the incubation. The experiment was partitioned into three phases (I, II, and III) based on the total organic carbon consumption rates from 7.0 ± 1.0 to 1.0 ± 0.1 and to 0.1 ± 0.0 μmol C L-1 day-1, respectively. Diverse generalists with low abundance were present in all three phases of the experiment, while a few abundant specialists dominated specific phases, suggesting their diverse roles in the transformation of DOM molecules from labile and semilabile to recalcitrant. The changes of organic molecules belonging to CHO, CHNO, and CHOS containing formulas were closely associated with specific microbial populations, suggesting close interactions between the different bacterial metabolic potential for substrates and DOM molecular compositional characteristics. This study sheds light on the interactions between microbial population succession and DOM molecular changes processes and collectively advances our understanding of microbial processing of the marine elemental cycle. IMPORTANCE Phytoplankton are a major contributor of labile dissolved organic matter (DOM) in the upper ocean, fueling tremendous marine prokaryotic activity. Interactions between microorganisms and algae-derived DOM regulate biogeochemical cycles in the ocean, but key aspects of their interactions remain poorly understood. Under global warming and eutrophication scenarios, Synechococcus blooms are commonly observed in coastal seawaters, and they significantly influence the elemental biogeochemistry cycling in eutrophic ecosystems. To understand the interactions between Synechococcus-derived DOM and heterotrophic prokaryotes as well as their influence on the coastal environment, we investigated the degradation of DOM by coastal microbes during a 180-day dark incubation. We showed substantial DOM compositional changes that were closely linked to the developments of microbial specialists and generalists. Our study provides information on the interactions between microbial population succession and DOM molecular changes, thereby advancing our understanding of microbial processing of the marine DOM pool under the influence of climate change.

Effects of Temperature and Nitrogen Application on Carbon and Nitrogen Accumulation and Bacterial Community Composition in Apple Rhizosphere Soil

Malus sieversii grows on the slopes of the Tianshan Mountains in Xinjiang where the difference in daily temperature is significant. In recent years, the rhizosphere soil health of Malus sieversii has been severely impacted by anthropogenic disturbance and pathogenic infestation. The soil nutrient content and soil microorganism diversity are the main components of soil health. Low temperature has negative effects on soil bacterial community structure by inhibiting the accumulation of carbon and nitrogen. However, the effects of temperature and nitrogen application on soil carbon and nitrogen accumulation and the bacterial community composition in the rhizosphere soil of Malus sieversii are unclear. We set two temperature levels, i.e., low temperature (L) and room temperature (R), combined with no nitrogen (N0) and nitrogen application (N1) to explore the response of plant carbon and nitrogen uptake, rhizosphere soil carbon and nitrogen accumulation and bacterial community composition to temperature and nitrogen fertilization. At the same temperature level, plant 13C abundance (P-Atom13C), plant 15N absolute abundance (P-Con15N), soil 15N abundance (S-Atom15N) and soil urease, protease and glutaminase activities were significantly higher under nitrogen application compared with the no-nitrogen application treatment. The bacterial community diversity and richness indices of the apple rhizosphere soil in the N1 treatment were higher than those in the N0 treatment. The relative abundances of Actinobacteria, Rhodopseudomonas, and Bradyrhizobium were higher in the LN1 treatment than in the LN0 treatment. Redundancy analysis (RDA) showed that plant 13C absolute abundance (P-Con13C) and plant 15N absolute abundance (P-Con15N) were the main factors affecting the soil bacterial community composition. In summary, Nitrogen application can alleviate the effects of low temperature stress on the soil bacterial community and is of benefit for the uptakes of carbon and nitrogen in Malus sieversii plants.

Variations and Mutual Relations of Vegetation–Soil–Microbes of Alpine Meadow in the Qinghai-Tibet Plateau under Degradation and Cultivation

Artificial cultivation had been applied to recover the meadow suffering from serious degradation in the Qinghai–Tibet Plateau. Studies focusing only on the changes in vegetation, soil and microbes along the meadow degradation were insufficient, and artificial cultivation as an important part of succession was always neglected. Here, the variables of vegetation, soil, and soil bacteria are surveyed in four types of alpine meadow in the protected lands of the Qinghai–Tibet Plateau: intact alpine meadow (IAM), moderate degradation alpine meadow (MDAM), extreme degradation alpine meadow (black soil beach (BSB)), and artificial alpine grassland (AAG). The results indicated that degradation and cultivation significantly changed the characteristics of the vegetation community, physicochemical features of the soil, and soil bacterial community diversity. Soil bacteria took a considerably longer time to adapt to degradation and cultivation than vegetation and soil. Compared to IAM and BSB, ADAM and AAG had more specific bacteria identified by ANOVA and LEfSe analysis, implying an unstable state. Combined with vegetation and soil variables, it was speculated that the unstable AAG was not significantly improved from the degraded meadow, and also lagged significantly compared to IAM. Correlation analysis revealed that aboveground biomass, species richness, vegetation coverage, SOC, C/N, BD, WC, and pH were significantly associated with bacterial diversity under community level. Aboveground biomass was an effective indicator for soil bacterial gene copies. Redundancy analysis demonstrated that the soil bacterial community is mainly regulated by the vegetation coverage, Gleason index, Simpson index, TN, TP, and pH under phylum and genus level. Partial mantel test analysis indicated that the physicochemical features of the soil were the most important factor correlating with the soil bacterial community along the degradation and cultivation, compared to other environmental factors.

Microbial Assemblage Dynamics Within the American Alligator Nesting Ecosystem: a Comparative Approach Across Ecological Scales

Understanding the ecological processes that shape species assemblage patterns is central to community ecology. The effects of ecological processes on assemblage patterns are scale-dependent. We used metabarcoding and shotgun sequencing to determine bacterial taxonomic and functional assemblage patterns among varying defined focal scales (micro-, meso-, and macroscale) within the American alligator (Alligator mississippiensis) nesting microbiome. We correlate bacterial assemblage patterns among eight nesting compartments within and proximal to alligator nests (micro-), across 18 nests (meso-), and between 4 geographic sampling sites (macro-), to determine which ecological processes may drive bacterial assemblage patterns within the nesting environment. Among all focal scales, bacterial taxonomic and functional richness (α-diversity) did not statistically differ. In contrast, bacterial assemblage structure (β-diversity) was unique across all focal scales, whereas functional pathways were redundant within nests and across geographic sites. Considering these observed scale-based patterns, taxonomic bacterial composition may be governed by unique environmental filters and dispersal limitations relative to microbial functional attributes within the alligator nesting environment. These results advance pattern-process dynamics within the field of microbial community ecology and describe processes influencing the American alligator nest microbiome.

Moderate grazing increased alpine meadow soils bacterial abundance and diversity index on the Tibetan Plateau

The response of grassland soil bacterial community characteristics to different grazing intensities is central ecological topics. However, the underlying mechanisms between bacterial abundance, diversity index, and grazing intensity remain unclear. We measured alpine meadow soil bacterial gene richness and diversity index under four grazing intensities using 16S rDNA sequence analysis on the Tibetan Plateau. The results suggest that extreme grazing significantly decreased alpine meadow both bacterial gene abundance and diversity index (p < .05). The lowest operational taxonomic unit numbers were 3,012 ± 447 copies under heavy grazing in the growing season. It was significantly lower than heavy grazing with approximately 3,958 ± 119 copies (p < .05). The Shannon index for medium and high grazing grassland bacterial diversity was slightly higher than for light grazing in the growing season. Furthermore, the lowest index was approximately 9.20 ± 0.50 for extreme grazing of grassland in the growing season. The average bacterial gene abundance and diversity index in the dormancy period were slightly higher than that in the growing season. Soil bulk density, pH, ammonium, and nitrate nitrogen were the main positive factors driving grazed grassland bacterial communities. Our study provides insight into the response of alpine meadows to grazing intensity, demonstrating that moderate grazing increases bacterial community diversity in grazed grasslands.

Elevation rather than season determines the assembly and co-occurrence patterns of soil bacterial communities in forest ecosystems of Mount Gongga

Seasonal dynamics of soil microbial communities may influence ecosystem functions and services. However, few observations have been conducted on the dynamics of a bacterial community assembly across seasons in different elevations in mountain forest ecosystems. In this study, the diversity, compositions, community assembly processes, and co-occurrence interactions of soil bacterial communities were investigated using Illumina sequencing of 16S rRNA genes across different seasons during two consecutive years (2016 and 2017) at two elevational sites in Mount Gongga, China. These two sites included an evergreen broad-leaved forest (EBF, 2100 m a.s.l.) and a dark coniferous forest (DCF, 3000 m a.s.l.). The results showed that bacterial diversity and structure varied considerably between the two elevational sites with only limited seasonal variations. Interannuality had a significant effect on the diversity and structure of soil bacterial communities. The bacterial alpha diversity was significantly higher at site EBF(e.g., OTUs richness, 2207 ± 276) than at site DCF(e.g., OTUs richness, 1826 ± 315). Soil pH, temperature, elevation, and water content were identified as important factors shaping soil bacterial communities in the mountain forests. Bacterial community assembly was primarily governed by deterministic processes regardless of elevation and season. Deterministic processes were stronger at site DCF than at EBF. The soil bacterial community at site EBF harbored a more complex and connected network with less resistance to environmental changes. Overall, this study showed that seasonal dynamics of bacterial communities were much weaker than those along elevations, implying that a single-season survey on a bacterial community along an elevational gradient can represent overall changes in the bacterial community. KEY POINTS: • Seasonal dynamics of soil bacterial communities were studied in Mount Gongga. • The bacterial community was mainly affected by elevation rather than season. • Deterministic processes dominated bacterial community assembly. • The bacterial network was more complex but less stable at EBF than at DCF.

Fitness and Productivity Increase with Ecotypic Diversity among Escherichia coli Strains That Coevolved in a Simple, Constant Environment

The productivity of a biological community often correlates with its diversity. In the microbial world this phenomenon can sometimes be explained by positive, density-dependent interactions such as cross-feeding and syntrophy. These metabolic interactions help account for the astonishing variety of microbial life and drive many of the biogeochemical cycles without which life as we know it could not exist. While it is difficult to recapitulate experimentally how these interactions evolved among multiple taxa, we can explore in the laboratory how they arise within one. These experiments provide insight into how different bacterial ecotypes evolve and from these, possibly new "species." We have previously shown that in a simple, constant environment a single clone of Escherichia coli can give rise to a consortium of genetically and phenotypically differentiated strains, in effect, a set of ecotypes, that coexist by cross-feeding. We marked these different ecotypes and their shared ancestor by integrating fluorescent protein into their genomes and then used flow cytometry to show that each evolved strain is more fit than the shared ancestor, that pairs of evolved strains are fitter still, and that the entire consortium is the fittest of all. We further demonstrate that the rank order of fitness values agrees with estimates of yield, indicating that an experimentally evolved consortium more efficiently converts primary and secondary resources to offspring than its ancestor or any member acting in isolation.IMPORTANCE Polymicrobial consortia occur in both environmental and clinical settings. In many cases, diversity and productivity correlate in these consortia, especially when sustained by positive, density-dependent interactions. However, the evolutionary history of such entities is typically obscure, making it difficult to establish the relative fitness of consortium partners and to use those data to illuminate the diversity-productivity relationship. Here, we dissect an Escherichia coli consortium that evolved under continuous glucose limitation in the laboratory from a single common ancestor. We show that a partnership consisting of cross-feeding ecotypes is better able to secure primary and secondary resources and to convert those resources to offspring than the ancestral clone. Such interactions may be a prelude to a special form of syntrophy and are likely determinants of microbial community structure in nature, including those having clinical significance such as chronic infections.