Climate change legacies contrastingly affect the resistance and resilience of soil microbial communities and multifunctionality to extreme drought

The role of edaphic variables and management practices in regulating soil microbial resilience to drought - A meta-analysis

Environmental disturbances such as drought can impact soil health and the resistance (ability to withstand environmental stress) and resilience (ability to recover functional and structural integrity after stress) of soil microbial functional activities. A paucity of information exists on the impact of drought on soil microbiome and how soil biological systems respond to and demonstrate resilience to drought stress. To address this, we conducted a systematic review and meta-analysis (using only laboratory studies) to assess the response of soil microbial biomass and respiration to drought stress across agriculture, forest, and grassland ecosystems. The meta-analysis revealed an overall negative response of microbial biomass in resistance (-31.6 %) and resilience (-0.3 %) to drought, suggesting a decrease in soil microbial biomass content. Soil microbial respiration also showed a negative response in resistance to drought stress indicating a decrease in soil microbial respiration in agriculture (-17.5 %), forest (-64.0 %), and grassland (-65.5 %) ecosystems. However, it showed a positive response in resilience to drought, suggesting an effective recovery in microbial respiration post-drought. Soil organic carbon (SOC), clay content, and pH were the main regulating factors of the responses of soil microbial biomass and respiration to drought. In agriculture ecosystem, soil pH was primarily correlated with soil microbial respiration resistance and resilience to drought, potentially influenced by frequent land preparation and fertilizer applications, while in forest ecosystem SOC, clay content, and pH significantly impacted microbial biomass and respiration resistance and resilience. In grassland ecosystem, SOC was strongly associated with biomass resilience to drought. The impact of drought stress on soil microbiome showed different patterns in natural and agriculture ecosystems, and the magnitude of microbial functional responses regulated by soil intrinsic properties. This study highlighted the importance of understanding the role of soil properties in shaping microbial responses to drought stress for better ecosystem management.

Temperature-dependent effects of microplastics on sediment bacteriome and metabolome

The increasing prevalence of microplastics in the environment has become a concern for various ecosystems, including wetland ecosystems. Here, we investigated the effects of three popular microplastic types: polyethylene, polylactic acid, and tire particles at 5 °C and 25 °C on the sediment microbiome and metabolome at the 3% (w/w) level. Results indicated that temperature greatly influenced catalase and neutral phosphatase activities, whereas the type of microplastic had a more significant impact on urease and dehydrogenase activities. The addition of microplastic, especially tire particles, increased microbial diversity and significantly altered the microbial community structure and metabolic profile, leading to the formation of different clusters of microbial communities depending on the temperature. Nonetheless, the effect of temperature on the metabolite composition was less significant. Functional prediction showed that the abundance of functional genes related to metabolism and biogeochemical cycling increased with increasing temperature, especially the tire particles treatment group affected the nitrogen cycling by inhibiting ureolysis and nitrogen fixation. These observations emphasize the need to consider microplastic type and ambient temperature to fully understand the ecological impact of microplastics on microbial ecosystems.

Microbial network structure, not plant and microbial community diversity, regulates multifunctionality under increased precipitation in a cold steppe

It is known that the dynamics of multiple ecosystem functions (i. e., multifunctionality) are positively associated with microbial diversity and/or biodiversity. However, how the relationship between microbial species affects ecosystem multifunctionality remains unclear, especially in the case of changes in precipitation patterns. To explore the contribution of biodiversity and microbial co-occurrence networks to multifunctionality, we used rainfall shelters to simulate precipitation enhancement in a cold steppe in Northeast China over two consecutive growing seasons. We showed that an increased 50% precipitation profoundly reduced bacterial diversity and multidiversity, while inter-annual differences in precipitation did not shift microbial diversity, plant diversity, or multidiversity. Our analyses also revealed that increased annual precipitation significantly increased ecosystem, soil, nitrogen, and phosphorous cycle multifunctionality. Neither increased precipitation nor inter-annual differences in precipitation had a significant effect on carbon cycle multifunctionality, probably due to the relatively short period (2 years) of our experiment. The co-occurrence network of bacterial and fungal communities was the most dominant factor affecting multifunctionality, the numbers of negative interactions but not positive interactions were linked to multifunctionality. In particular, our results provided evidence that microbial network topological features are crucial for maintaining ecosystem functions in grassland ecosystems, which should be considered in related studies to accurately predict the responses of ecosystem multifunctionality to predicted changes in precipitation patterns.

Root endophytic bacterial and fungal communities in a natural hot desert are differentially regulated in dry and wet seasons by stochastic processes and functional traits

Dryland ecosystems experience seasonal cycles of severe drought and moderate precipitation. Desert plants may develop symbiotic relationships with root endophytic microbes to survive under the repeated wet and extremely dry conditions. Although community coalescence has been found in many systems, the colonization by functional microbes and its relationship to seasonal transitions in arid regions are not well understood. Here we examined root endophytic microbial taxa, and their traits in relation to their root colonization, during the dry and wet seasons in a hot desert of the southwestern United States. We used high-throughput DNA sequencing of 16S rRNA and internal transcribed spacer gene profiling of five desert shrubs, and analyzed the seasonal change in endophytic microbial lineages. Goodness of fit to the neutral community model in relationship to microbial traits was evaluated. In summer, Actinobacteria and Bacteroidia increased, although this was not genus-specific. For fungi, Glomeraceae selectively increased in summer. In winter, Gram-negative bacterial genera, including those capable of nitrogen fixation and plant growth promotion, increased. Neutral model analysis revealed a strong stochastic influence on endophytic bacteria but a weak effect for fungi, especially in summer. The taxa with higher frequency than that predicted by neutral model shared environmental adaptability and symbiotic traits, whereas the frequency of pathogenic fungi was at or under the predicted value. These results suggest that community assembly of bacteria and fungi is regulated differently. The bacterial community was affected by stochastic and deterministic processes via bacterial response to drought (response trait), beneficial effect on plants (effect trait), and likely stable mutualistic interactions with plants suggested by the frequency of nodule bacteria. For fungi, mycorrhizal fungi were selected by plants in summer. The regulation of beneficial microbes by plants in both dry and wet seasons suggests the presence of plant-soil positive feedback in this natural desert ecosystem.

Shift from flooding to drying enhances the respiration of soil aggregates by changing microbial community composition and keystone taxa

Changes in the water regime are among the crucial factors controlling soil carbon dynamics. However, at the aggregate scale, the microbial mechanisms that regulate soil respiration under flooding and drying conditions are obscure. In this research, we investigated how the shift from flooding to drying changes the microbial respiration of soil aggregates by affecting microbial community composition and their co-occurrence patterns. Soils collected from a riparian zone of the Three Gorges Reservoir, China, were subjected to a wet-and-dry incubation experiment. Our data illustrated that the shift from flooding to drying substantially enhanced soil respiration for all sizes of aggregate fractions. Moreover, soil respiration declined with aggregate size in both flooding and drying treatments. The keystone taxa in bacterial networks were found to be Acidobacteriales, Gemmatimonadales, Anaerolineales, and Cytophagales during the flooding treatment, and Rhizobiales, Gemmatimonadales, Sphingomonadales, and Solirubrobacterales during the drying treatment. For fungal networks, Hypocreales and Agaricalesin were the keystone taxa in the flooding and drying treatments, respectively. Furthermore, the shift from flooding to drying enhanced the microbial respiration of soil aggregates by changing keystone taxa. Notably, fungal community composition and network properties dominated the changes in the microbial respiration of soil aggregates during the shift from flooding to drying. Thus, our study highlighted that the shift from flooding to drying changes keystone taxa, hence increasing aggregate-scale soil respiration.

Variation in Temperature Dependences across Europe Reveals the Climate Sensitivity of Soil Microbial Decomposers

Temperature is a major determinant of biological process rates, and microorganisms are key regulators of ecosystem carbon (C) dynamics. Temperature controls microbial rates of decomposition, and thus warming can stimulate C loss, creating positive feedback to climate change. If trait distributions that define temperature relationships of microbial communities can adapt to altered temperatures, they could modulate the strength of this feedback, but if this occurs remains unclear. In this study, we sampled soils from a latitudinal climate gradient across Europe. We established the temperature relationships of microbial growth and respiration rates and used these to investigate if and with what strength the community trait distributions for temperature were adapted to their local environment. Additionally, we sequenced bacterial and fungal amplicons to link the variance in community composition to changes in temperature traits. We found that microbial temperature trait distributions varied systematically with climate, suggesting that an increase in mean annual temperature (MAT) of 1°C will result in warm-shifted microbial temperature trait distributions equivalent to an increase in temperature minimum (T_min) of 0.20°C for bacterial growth, 0.07°C for fungal growth, and 0.10°C for respiration. The temperature traits for bacterial growth were thus more responsive to warming than those for respiration and fungal growth. The microbial community composition also varied with temperature, enabling the interlinkage of taxonomic information with microbial temperature traits. Our work shows that the adaptation of microbial temperature trait distributions to a warming climate will affect the C-climate feedback, emphasizing the need to represent this to capture the microbial feedback to climate change. IMPORTANCE One of the largest uncertainties of global warming is if the microbial decomposer feedback will strengthen or weaken soil C-climate feedback. Despite decades of research effort, the strength of this feedback to warming remains unknown. We here present evidence that microbial temperature relationships vary systematically with environmental temperatures along a climate gradient and use this information to forecast how microbial temperature traits will create feedback between the soil C cycle and climate warming. We show that the current use of a universal temperature sensitivity is insufficient to represent the microbial feedback to climate change and provide new estimates to replace this flawed assumption in Earth system models. We also demonstrate that temperature relationships for rates of microbial growth and respiration are differentially affected by warming, with stronger responses to warming for microbial growth (soil C formation) than for respiration (C loss from soil to atmosphere), which will affect the atmosphere-land C balance.

The soil microbiomes of forest ecosystems in Kenya: their diversity and environmental drivers

Soil microbiomes in forest ecosystems act as both nutrient sources and sinks through a range of processes including organic matter decomposition, nutrient cycling, and humic compound incorporation into the soil. Most forest soil microbial diversity studies have been performed in the northern hemisphere, and very little has been done in forests within African continent. This study examined the composition, diversity and distribution of prokaryotes in Kenyan forests top soils using amplicon sequencing of V4-V5 hypervariable region of the 16S rRNA gene. Additionally, soil physicochemical characteristics were measured to identify abiotic drivers of prokaryotic distribution. Different forest soils were found to have statistically distinct microbiome compositions, with Proteobacteria and Crenarchaeota taxa being the most differentially abundant across regions within bacterial and archaeal phyla, respectively. Key bacterial community drivers included pH, Ca, K, Fe, and total N while archaeal diversity was shaped by Na, pH, Ca, total P and total N. To contextualize the prokaryote diversity of Kenyan forest soils on a global scale, the sample set was compared to amplicon data obtained from forest biomes across the globe; displaying them to harbor distinct microbiomes with an over-representation of uncultured taxa such as TK-10 and Ellin6067 genera.

Soil nematode abundances drive agroecosystem multifunctionality under short-term elevated CO2 and O3

The response of soil biotas to climate change has the potential to regulate multiple ecosystem functions. However, it is still challenging to accurately predict how multiple climate change factors will affect multiple ecosystem functions. Here, we assessed the short-term responses of agroecosystem multifunctionality to a factorial combination of elevated CO₂ (+200 ppm) and O₃ (+40 ppb) and identified the key soil biotas (i.e., bacteria, fungi, protists, and nematodes) concerning the changes in the multiple ecosystem functions for two rice varieties (Japonica, Nanjing 5055 vs. Wuyujing 3). We provided strong evidence that combined treatment rather than individual treatments of short-term elevated CO₂ and O₃ significantly increased the agroecosystem multifunctionality index by 32.3% in the Wuyujing 3 variety, but not in the Nanjing 5055 variety. Soil biotas exhibited an important role in regulating multifunctionality under short-term elevated CO₂ and O₃ , with soil nematode abundances better explaining the changes in ecosystem multifunctionality than soil biota diversity. Furthermore, the higher trophic groups of nematodes, omnivores-predators served as the principal predictor of agroecosystem multifunctionality. These results provide unprecedented new evidence that short-term elevated CO₂ and O₃ can potentially affect agroecosystem multifunctionality through soil nematode abundances, especially omnivores-predators. Our study demonstrates that high trophic groups were specifically beneficial for regulating multiple ecosystem functions and highlights the importance of soil nematode communities for the maintenance of agroecosystem functions and health under climate change in the future.

Biogeographical survey of soil microbiomes across sub-Saharan Africa: structure, drivers, and predicted climate-driven changes

BACKGROUND

Top-soil microbiomes make a vital contribution to the Earth's ecology and harbor an extraordinarily high biodiversity. They are also key players in many ecosystem services, particularly in arid regions of the globe such as the African continent. While several recent studies have documented patterns in global soil microbial ecology, these are largely biased towards widely studied regions and rely on models to interpolate the microbial diversity of other regions where there is low data coverage. This is the case for sub-Saharan Africa, where the number of regional microbial studies is very low in comparison to other continents.

RESULTS

The aim of this study was to conduct an extensive biogeographical survey of sub-Saharan Africa's top-soil microbiomes, with a specific focus on investigating the environmental drivers of microbial ecology across the region. In this study, we sampled 810 sample sites across 9 sub-Saharan African countries and used taxonomic barcoding to profile the microbial ecology of these regions. Our results showed that the sub-Saharan nations included in the study harbor qualitatively distinguishable soil microbiomes. In addition, using soil chemistry and climatic data extracted from the same sites, we demonstrated that the top-soil microbiome is shaped by a broad range of environmental factors, most notably pH, precipitation, and temperature. Through the use of structural equation modeling, we also developed a model to predict how soil microbial biodiversity in sub-Saharan Africa might be affected by future climate change scenarios. This model predicted that the soil microbial biodiversity of countries such as Kenya will be negatively affected by increased temperatures and decreased precipitation, while the fungal biodiversity of Benin will benefit from the increase in annual precipitation.

CONCLUSION

This study represents the most extensive biogeographical survey of sub-Saharan top-soil microbiomes to date. Importantly, this study has allowed us to identify countries in sub-Saharan Africa that might be particularly vulnerable to losses in soil microbial ecology and productivity due to climate change. Considering the reliance of many economies in the region on rain-fed agriculture, this study provides crucial information to support conservation efforts in the countries that will be most heavily impacted by climate change. Video Abstract.