The metamicrobiome: key determinant of the homeostasis of nutrient recycling

Close neighbors, not intruders: investigating the role of tank bromeliads in shaping faunal microbiomes

Background

Tropical montane cloud forests contain high levels of epiphyte diversity. Epiphytic tank bromeliads play an important role in the functioning of these ecosystems and provide a microhabitat for many species of invertebrates. Microbial ecology theory suggests that the environment serves as a source of microbes for animals, but the contribution of this factor to the composition of an animal microbiome varies. In this study, we examined the extent to which tank bromeliads (Tillandsia multicaulis) serve as a source of microbes for two species of fly larvae in a cloud forest fragment in central Veracruz, Mexico.

Methods

We used 16S rRNA sequencing to characterize the bacterial communities in the organic matter within bromeliad tanks and in the whole bodies (surface and gut) of larvae from two fly taxa (Austrophorocera sp., Tachinidae, and Copestylum sp., Syrphidae) that inhabit these bromeliads. To assess the contribution of bromeliads to the microbiome of the fly larvae, we conducted fast expectation-maximization microbial source tracking (FEAST) analysis.

Results

The bacterial communities in bromeliad tanks were primarily composed of Pseudomonadota, Acidobacteriota, Bacteroidota, Verrucomicrobiota, and Spirochaetota. Similarly, communities of the fly larvae contained Pseudomonadota, Bacteroidota, Bacillota, and Actinomycetota. Bromeliad tanks exhibited the highest bacterial richness, followed by Copestylum and Austrophorocera larvae. Beta diversity analyses indicated that bacterial communities clustered by species. We found a modest contribution of bromeliads to the fly microbiome, with nearly 30% of the larvae microbiome traced to the organic matter deposited in the tanks.

Conclusions

Our data suggest that the microbiome of flies, which inhabit tank bromeliads during their larval stage, is nourished to some extent by the bacterial communities present in the organic matter within the tank.

Structural and Functional Characteristics of Soil Microbial Communities in Forest-Wetland Ecotones: A Case Study of the Lesser Khingan Mountains

Soil microorganisms play an essential role in vegetation succession, nutrient cycling, and ecosystem restoration. This study investigates the responses of soil microbial communities to ecological transitions from forest to wetland in the Lesser Khingan Mountains, including mixed forest, conifer forest, wetland edge, and natural wetland. The results indicated that natural wetland soils were weakly acidic and contained significantly higher organic matter, total nitrogen, and available phosphorus compared to other soils. Soil bulk density increased with depth. Actinobacteria, Acidobacteriota, and Proteobacteria dominated in mixed forest, wetland edge, and natural wetland soils, respectively, showing minimal variation between depths. Principal component analysis and non-metric multidimensional scaling demonstrated distinct bacterial communities between natural wetlands and wetland edges. Redundancy analysis revealed that soil bacterial communities differed significantly between 15 cm and 30 cm layers, influenced by potassium, bulk density, organic carbon, phosphorus, and nitrogen. Proteobacteria and Bacteroidota abundances correlated positively with nutrients, while Acidobacteriota and Verrucomicrobiota correlated negatively with available potassium. Chemotrophic and aerobic bacteria dominated in forest soils, whereas fermentation-related and anaerobic bacteria were prevalent in wetland soils. The study highlights how ecological transitions and soil properties shape soil microbial communities and their functions.

The gills and skin microbiota of five pelagic fish species from the Atlantic Ocean

The gills and skin microbiota and microbiome of wild fish remain far more under-investigated compared to that of farmed fish species, despite that these animal-microbe interactions hold the same ecophysiological roles in both cases. In this study, the gills and skin bacterial microbiota profiles and their presumptive bacterial metabolisms were investigated in five open-sea fishes: bullet tuna (Auxis sp.), common dolphinfish (Coryphaena hippurus), Atlantic little tunny (Euthynnus alletteratus), Atlantic bonito (Sarda sarda) and Atlantic white marlin (Kajikia albida). Gills and skin tissues were collected from two to three individuals per species, from specimens caught by recreational trolling during summer of 2019, and their bacterial 16S rRNA gene diversity was analysed by high-throughput sequencing. The gills bacterial communities among the five species were clearly different but not the skin bacterial microbiota. The dominant operational taxonomic units belonged to the Moraxellaceae, Pseudomonadaceae, Rhodobacteraceae, Staphylococcaceae and Vibrionaceae families. Despite the differences in taxonomic composition, the presumptive bacterial metabolisms between the gills and skin of the five fishes investigated here were ≥ 94% similar and were dominated by basic metabolism, most likely reflecting the continuous exposure of these tissues in the surrounding seawater.

Regulation of drought stress on nutrient cycle and metabolism of rhizosphere microorganisms in desert riparian forest

Microbial communities in desert riparian forest ecosystems have developed unique adaptive strategies to thrive in harsh habitats shaped by prolonged exposure to abiotic stressors. However, the influence of drought stress on the functional and metabolic characteristics of soil rhizosphere microorganisms remains unknown. Therefore, this study aimed to investigate the effects of drought stress on soil biogeochemistry and metabolism and analyze the relationship between the biogeochemical cycle processes and network of differentially-expressed metabolites. Using metagenomics and metabolomics, this study explored the microbial functional cycle and differential metabolic pathways within desert riparian forests. The predominant biogeochemical cycles in the study area were the Carbon and Nitrogen cycles, comprising 78.90 % of C, N, Phosphorus, Sulfur and Iron cycles. Drought led to increased soil C fixation, reduced C degradation and methane metabolism, weakened denitrification, and decreased N fixation. Furthermore, drought can disrupt iron homeostasis and reduce its absorption. The differential metabolic pathways of drought stress include flavonoid biosynthesis, arachidonic acid metabolism, steroid hormone biosynthesis, and starch and sucrose degradation. Network analysis of functional genes and metabolism revealed a pronounced competitive relationship between the C cycle and metabolic network, whereas the Fe cycle and metabolic network promoted each other, optimizing resource utilization. Partial least squares analysis revealed that drought hindered the expression and metabolic processes and functional genes, whereas the rhizosphere environment facilitated metabolic expression and the functional genes. The rhizosphere effect primarily promoted metabolic processes indirectly through soil enzyme activities. The integrated multi-omics analysis further revealed that the effects of drought and the rhizosphere play a predominant role in shaping soil functional potential and the accumulation of metabolites. These insights deepen our comprehension of desert riparian forest ecosystems and offer strong support for the functionality of nutrient cycling and metabolite dynamics.

Impact of elevated CO2 on microbial communities and functions in riparian sediments: Role of pollution levels in modulating effects

The impact of elevated CO2 levels on microorganisms is a focal point in studying the environmental effects of global climate change. A growing number of studies have demonstrated the importance of the direct effects of elevated CO2 on microorganisms, which are confounded by indirect effects that are not easily identified. Riparian zones have become key factor in identifying the environmental effects of global climate change because of their special location. However, the direct effects of elevated CO2 levels on microbial activity and function in riparian zone sediments remain unclear. In this study, three riparian sediments with different pollution risk levels of heavy metals and nutrients were selected to explore the direct response of microbial communities and functions to elevated CO2 excluding plants. The results showed that the short-term effects of elevated CO2 did not change the diversity of the bacterial and fungal communities, but altered the composition of their communities. Additionally, differences were observed in the responses of microbial functions to elevated CO2 levels among the three regions. Elevated CO2 promoted the activities of nitrification and denitrification enzymes and led to significant increases in N2O release in the three sediments, with the greatest increase of 76.09 % observed in the Yuyangshan Bay (YYS). Microbial carbon metabolism was promoted by elevated CO2 in YYS but was significantly inhibited by elevated CO2 in Gonghu Bay and Meiliang Bay. Moreover, TOC, TN, and Pb contents were identified as key factors contributing to the different microbial responses to elevated CO2 in sediments with different heavy metal and nutrient pollution. In conclusion, this study provides in-depth insights into the responses of bacteria and fungi in polluted riparian sediments to elevated CO2, which helps elucidate the complex interactions between microbial activity and environmental stressors.

Litter quality and climate regulate the effect of invertebrates on litter decomposition in terrestrial and aquatic ecosystems: A global meta-analysis

Although the exclusion effects of invertebrate decomposers on litter decomposition have been extensively studied in different experimental contexts, a thorough comparison of the exclusion effects of invertebrate decomposers with different body sizes on litter decomposition and its possible regulatory factors in terrestrial and aquatic ecosystems is still lacking. Here, through a meta-analysis of 1207 pairs of observations from 110 studies in terrestrial ecosystems and 473 pairs of observations from 60 studies in aquatic ecosystems, we found that invertebrate exclusion reduced litter decomposition rates by 36 % globally, 30 % in terrestrial ecosystems, and 44 % in aquatic ecosystems. At the global scale, the exclusion effects of macroinvertebrates and mesoinvertebrates on litter decomposition rates (reduced by 38 % and 36 %, respectively) were greater than those of the combination of macroinvertebrates and mesoinvertebrates (reduced by 30 %). In terrestrial and aquatic ecosystems, the effects of invertebrate exclusion on litter decomposition rates were mainly regulated by climate and initial litter quality, but the effects of invertebrate exclusion with different body sizes were regulated differently by climate, initial litter quality, and abiotic environmental variables. These findings will help us better understand the role of invertebrate decomposers in litter decomposition, especially for invertebrate decomposers with different body sizes, and underscore the need to incorporate invertebrate decomposers with different body sizes into dynamic models of litter decomposition to examine the potential effects and regulatory mechanisms of land-water-atmosphere carbon fluxes.

Global contribution of invertebrates to forest litter decomposition

Forest litter decomposition is an essential component of global carbon and nutrient turnover. Invertebrates play important roles in litter decomposition, but the regional pattern of their effects is poorly understood. We examined 476 case studies across 93 sites and performed a meta-analysis to estimate regional effects of invertebrates on forest litter decomposition. We then assessed how invertebrate diversity, climate and soil pH drive regional variations in invertebrate-mediated decomposition. We found that (1) invertebrate contributions to litter decomposition are 1.4 times higher in tropical and subtropical forests than in forests elsewhere, with an overall contribution of 31% to global forest litter decomposition; and (2) termite diversity, together with warm, humid and acidic environments in the tropics and subtropics are positively associated with forest litter decomposition by invertebrates. Our results demonstrate the significant difference in invertebrate effects on mediating forest litter decomposition among regions. We demonstrate, also, the significance of termites in driving litter mass loss in the tropics and subtropics. These results are particularly pertinent in the tropics and subtropics where climate change and human disturbance threaten invertebrate biodiversity and the ecosystem services it provides.

Economic microbiology: exploring microbes as agents in economic systems

Microbial communities exhibit striking parallels with economic markets, resembling intricate ecosystems where microorganisms engage in resource exchange akin to human market transactions. This dynamic network of resource swapping mirrors economic trade in human markets, with microbes specializing in metabolic functions much like businesses specializing in goods and services. Cooperation and competition are central dynamics in microbial communities, with alliances forming for mutual benefit and species vying for dominance, similar to businesses seeking market share. The human microbiome, comprising trillions of microorganisms within and on our bodies, is not only a marker of socioeconomic status but also a critical factor contributing to persistent health inequalities. Social and economic factors shape the composition of the gut microbiota, impacting healthcare access and quality of life. Moreover, these microbes exert indirect influence over human decisions by affecting neurotransmitter production, influencing mood, behavior, and choices related to diet and emotions. Human activities significantly impact microbial communities, from dietary choices and antibiotic use to environmental changes, disrupting these ecosystems. Beyond their natural roles, humans harness microbial communities for various applications, manipulating their interactions and resource exchanges to achieve specific goals in fields like medicine, agriculture, and environmental science. In conclusion, the concept of microbial communities as biological markets offers valuable insights into their intricate functioning and adaptability. It underscores the profound interplay between microbial ecosystems and human health and behavior, with far-reaching implications for multiple disciplines. To paraphrase Alfred Marshall, "the Mecca of the economist lies in economic microbiology."

New ways for (in)validating the forest carbon neutrality hypothesis

Over 50 years ago, Eugene Odum postulated that mature or climax forests reside in carbon neutrality. As climate change rose to prominence in the international environmental agenda, the neutrality hypothesis transformed from an ecological principle to a justification for using forest management in combating climate change. Despite persistent efforts, Odum's neutrality hypothesis has resisted both confirmation and refutation. In this opinion we show the limitations of past efforts to (in)validate Odum's neutrality hypothesis and propose new research directions for the community to permit a more general confirmation or refutation with current and near-future observations. We then demonstrate such an approach by using metabolic theory to formulate testable predictions for the total sink strength considering soil, litter, and biomass of mature or climax forests based on observations of tree biomass and individual density. In doing so, we show that ecological theory can create additional relevant, testable hypotheses to provide timely support to decision-makers seeking to address one of the world's most pressing environmental challenges.

Climate dependence of the macrofaunal effect on litter decomposition-A global meta-regression analysis

Litter decomposition by microorganisms and animals is influenced by climate and has been found to be higher in warm and wet than in cold and dry biomes. We, however, hypothesized that the macrofaunal effect on decomposition should increase with temperature and aridity since larger animals are more tolerant to aridity than smaller organisms. This hypothesis was supported by our global analysis of macrofauna exclusion studies. Macrofauna increased litter mass loss on average by 40%, twofold higher than the highest previous estimation of macrofaunal effect on decomposition. The strongest effect was found in subtropical deserts where faunal decomposition had not been considered important. Our results highlight the need to consider animal size when exploring climate dependence of faunal decomposition, and the disproportionately large role of macrofauna in regulating litter decomposition in warm drylands. This new realization is critical for understanding element cycling in the face of global warming and aridification.

Impacts of large herbivores on terrestrial ecosystems

Large herbivores play unique ecological roles and are disproportionately imperiled by human activity. As many wild populations dwindle towards extinction, and as interest grows in restoring lost biodiversity, research on large herbivores and their ecological impacts has intensified. Yet, results are often conflicting or contingent on local conditions, and new findings have challenged conventional wisdom, making it hard to discern general principles. Here, we review what is known about the ecosystem impacts of large herbivores globally, identify key uncertainties, and suggest priorities to guide research. Many findings are generalizable across ecosystems: large herbivores consistently exert top-down control of plant demography, species composition, and biomass, thereby suppressing fires and the abundance of smaller animals. Other general patterns do not have clearly defined impacts: large herbivores respond to predation risk but the strength of trophic cascades is variable; large herbivores move vast quantities of seeds and nutrients but with poorly understood effects on vegetation and biogeochemistry. Questions of the greatest relevance for conservation and management are among the least certain, including effects on carbon storage and other ecosystem functions and the ability to predict outcomes of extinctions and reintroductions. A unifying theme is the role of body size in regulating ecological impact. Small herbivores cannot fully substitute for large ones, and large-herbivore species are not functionally redundant - losing any, especially the largest, will alter net impact, helping to explain why livestock are poor surrogates for wild species. We advocate leveraging a broad spectrum of techniques to mechanistically explain how large-herbivore traits and environmental context interactively govern the ecological impacts of these animals.