ABSTRACT
Demographic studies measure drivers of plant fecundity including seed production and survival, but few address both abiotic and biotic drivers of germination such as variation in climate among sites, population density, maternal plants, seed type and fungal pathogen abundance. We examined germination and microbial communities of seeds of Danthonia californica, which are either chasmogamous (external, wind-pollinated) or cleistogamous (internal, self-fertilized) and Festuca roemeri, which are solely chasmogamous. Seed populations were sourced across environmental gradients. We tested germination and used high-throughput sequencing to characterize seed fungal community structure. For F. roemeri, maternal plants significantly influenced germination as did climate and pathogens; germination increased from wetter, cooler sites. For D. californica, the main drivers of germination were maternal plant, seed type and pathogens; on average, more chasmogamous seeds germinated. Fungal communities depended largely on seed type, with fewer fungi associated with cleistogamous seeds, but the communities also depended on site factors such as vapor pressure deficit, plant density and whether the seeds had germinated. Putative pathogens that were negatively correlated with germination were more abundant for both D. californica and F. roemeri chasmogamous seeds than D. californica cleistogamous seeds. In D. californica, cleistogamous and chasmogamous seeds contain vastly different fungal communities.
Subject(s)
Festuca , Mycobiome , Demography , Germination , Poaceae , SeedsABSTRACT
Numerous therapeutically relevant small molecules have been identified from the screening of natural products (NPs) produced by environmental bacteria. These discovery efforts have principally focused on culturing bacteria from natural environments rich in biodiversity. We sought to assess the biosynthetic capacity of urban soil environments using a phylogenetic analysis of conserved NP biosynthetic genes amplified directly from DNA isolated from New York City park soils. By sequencing genes involved in the biosynthesis of nonribosomal peptides and polyketides, we found that urban park soil microbiomes are both rich in biosynthetic diversity and distinct from nonurban samples in their biosynthetic gene composition. A comparison of sequences derived from New York City parks to genes involved in the biosynthesis of biomedically important NPs produced by bacteria originally collected from natural environments around the world suggests that bacteria producing these same families of clinically important antibiotics, antifungals, and anticancer agents are actually present in the soils of New York City. The identification of new bacterial NPs often centers on the systematic exploration of bacteria present in natural environments. Here, we find that the soil microbiomes found in large cities likely hold similar promise as rich unexplored sources of clinically relevant NPs.
Subject(s)
Bacteria/genetics , Parks, Recreational , Soil Microbiology , Soil/chemistry , Biodiversity , Biological Products , Drug Design , Metagenome , Microbiota , New York City , Phylogeny , Sequence Analysis, DNAABSTRACT
New York City (NYC) is pioneering green infrastructure with the use of bioswales and other engineered soil-based habitats to provide stormwater infiltration and other ecosystem functions. In addition to avoiding the environmental and financial costs of expanding traditional built infrastructure, green infrastructure is thought to generate cobenefits in the form of diverse ecological processes performed by its plant and microbial communities. Yet, although plant communities in these habitats are closely managed, we lack basic knowledge about how engineered ecosystems impact the distribution and functioning of soil bacteria. We sequenced amplicons of the 16S ribosomal subunit, as well as seven genes associated with functional pathways, generated from both total (DNA-based) and expressed (RNA) soil communities in the Bronx, NYC, NY, in order to test whether bioswale soils host characteristic bacterial communities with evidence for enriched microbial functioning, compared to nonengineered soils in park lawns and tree pits. Bioswales had distinct, phylogenetically diverse bacterial communities, including taxa associated with nutrient cycling and metabolism of hydrocarbons and other pollutants. Bioswale soils also had a significantly greater diversity of genes involved in several functional pathways, including carbon fixation (cbbL-R [cbbL gene, red-like subunit] and apsA), nitrogen cycling (noxZ and amoA), and contaminant degradation (bphA); conversely, no functional genes were significantly more abundant in nonengineered soils. These results provide preliminary evidence that urban land management can shape the diversity and activity of soil communities, with positive consequences for genetic resources underlying valuable ecological functions, including biogeochemical cycling and degradation of common urban pollutants.IMPORTANCE Management of urban soil biodiversity by favoring taxa associated with decontamination or other microbial metabolic processes is a powerful prospect, but it first requires an understanding of how engineered soil habitats shape patterns of microbial diversity. This research adds to our understanding of urban microbial biogeography by providing data on soil bacteria in bioswales, which had relatively diverse and compositionally distinct communities compared to park and tree pit soils. Bioswales also contained comparatively diverse pools of genes related to carbon sequestration, nitrogen cycling, and contaminant degradation, suggesting that engineered soils may serve as effective reservoirs of functional microbial biodiversity. We also examined both total (DNA-based) and expressed (RNA) communities, revealing that total bacterial communities (the exclusive targets in the vast majority of soil studies) were poor predictors of expressed community diversity, pointing to the value of quantifying RNA, especially when ecological functioning is considered.
Subject(s)
Bacteria/isolation & purification , Phylogeny , Soil Microbiology , Bacteria/classification , Bacteria/genetics , Bacteria/metabolism , Biodiversity , DNA, Bacterial/genetics , Hydrocarbons/metabolism , New York City , RNA, Bacterial/genetics , RNA, Ribosomal, 16S/genetics , Urban RenewalABSTRACT
Negative population feedbacks mediated by natural enemies can promote species coexistence at the community scale through disproportionate mortality of numerically dominant (common) tree species. Simultaneously, associations with arbuscular mycorrhizal fungi (AMF) can result in positive effects on tree populations. Coupling data on seedling foliar damage from herbivores and pathogens and DNA sequencing of soil AMF diversity, we assessed the effects of these factors on tree seedling mortality at local (1 m2 ) and community (16 ha plot) scales in a tropical rainforest in Puerto Rico. At the local scale, AMF diversity in soil counteracted negative effects from foliar damage on seedling mortality. At the community scale, mortality of seedlings of common tree species increased with foliar damage while rare tree species benefited from soil AMF diversity. Together, the effects of foliar damage and soil AMF diversity on seedling mortality might foster tree species coexistence in this forest.
Subject(s)
Forests , Mycorrhizae/classification , Seedlings/microbiology , Soil Microbiology , Trees/microbiology , Biodiversity , Mycorrhizae/physiology , Puerto RicoABSTRACT
Plants interact with a diversity of microorganisms, and there is often concordance in their community structures. Because most community-level studies are observational, it is unclear if such concordance arises because of host specificity, in which microorganisms or plants limit each other's occurrence. Using a reciprocal transplant experiment, we tested the hypothesis that host specificity between trees and ectomycorrhizal fungi determines patterns of tree and fungal soil specialisation. Seedlings of 13 dipterocarp species with contrasting soil specialisations were seeded into plots crossing soil type and canopy openness. Ectomycorrhizal colonists were identified by DNA sequencing. After 2.5 years, we found no evidence of host specificity. Rather, soil environment was the primary determinant of ectomycorrhizal diversity and composition on seedlings. Despite their close symbiosis, our results show that ectomycorrhizal fungi and tree communities in this Bornean rain forest assemble independently of host-specific interactions, raising questions about how mutualism shapes the realised niche.
Subject(s)
Mycorrhizae/classification , Soil Microbiology , Symbiosis , Trees/microbiology , Borneo , DNA, Fungal/genetics , Fungi/classification , Fungi/genetics , Linear Models , Mycorrhizae/genetics , Plant Roots/microbiology , Rainforest , Sequence Analysis, DNA , Soil , Trees/classification , Tropical ClimateABSTRACT
The complexities of the relationships between plant and soil microbial communities remain unresolved. We determined the associations between plant aboveground and belowground (root) distributions and the communities of soil fungi and bacteria found across a diverse tropical forest plot. Soil microbial community composition was correlated with the taxonomic and phylogenetic structure of the aboveground plant assemblages even after controlling for differences in soil characteristics, but these relationships were stronger for fungi than for bacteria. In contrast to expectations, the species composition of roots in our soil core samples was a poor predictor of microbial community composition perhaps due to the patchy, ephemeral, and highly overlapping nature of fine root distributions. Our ability to predict soil microbial composition was not improved by incorporating information on plant functional traits suggesting that the most commonly measured plant traits are not particularly useful for predicting the plot-level variability in belowground microbial communities.
Subject(s)
Bacterial Physiological Phenomena , Biodiversity , Fungi/physiology , Soil Microbiology , Trees/physiology , Microbiota , Panama , Plant Roots/physiology , Rainforest , Tropical ClimateABSTRACT
Although fungal communities are known to vary along latitudinal gradients, mechanisms underlying this pattern are not well-understood. We used high-throughput sequencing to examine the large-scale distributions of soil fungi and their relation to evolutionary history. We tested the Tropical Conservatism Hypothesis, which predicts that ancestral fungal groups should be more restricted to tropical latitudes and conditions than would more recently derived groups. We found support for this hypothesis in that older phyla preferred significantly lower latitudes and warmer, wetter conditions than did younger phyla. Moreover, preferences for higher latitudes and lower precipitation levels were significantly phylogenetically conserved among the six younger phyla, possibly because the older phyla possess a zoospore stage that is vulnerable to drought, whereas the younger phyla retain protective cell walls throughout their life cycle. Our study provides novel evidence that the Tropical Conservatism Hypothesis applies to microbes as well as plants and animals.
Subject(s)
Biological Evolution , Fungi/physiology , Soil Microbiology , Biodiversity , Ecosystem , Fungi/classification , Fungi/genetics , Phylogeny , RNA, Ribosomal, 18S/genetics , Tropical ClimateABSTRACT
Plant diversity is considered one factor structuring soil fungal communities because the diversity of compounds in leaf litter might determine the extent of resource heterogeneity for decomposer communities. Lowland tropical rain forests have the highest plant diversity per area of any biome. Since fungi are responsible for much of the decomposition occurring in forest soils, understanding the factors that structure fungi in tropical forests may provide valuable insight for predicting changes in global carbon and nitrogen fluxes. To test the role of plant diversity in shaping fungal community structure and function, soil (0-20 cm) and leaf litter (O horizons) were collected from six established 1-ha forest census plots across a natural plant diversity gradient on the Isthmus of Panama. We used 454 pyrosequencing and phospholipid fatty acid analysis to evaluate correlations between microbial community composition, precipitation, soil nutrients, and plant richness. In soil, the number of fungal taxa increased significantly with increasing mean annual precipitation, but not with plant richness. There were no correlations between fungal communities in leaf litter and plant diversity or precipitation, and fungal communities were found to be compositionally distinct between soil and leaf litter. To directly test for effects of plant species richness on fungal diversity and function, we experimentally re-created litter diversity gradients in litter bags with 1, 25, and 50 species of litter. After 6 months, we found a significant effect of litter diversity on decomposition rate between one and 25 species of leaf litter. However, fungal richness did not track plant species richness. Although studies in a broader range of sites is required, these results suggest that precipitation may be a more important factor than plant diversity or soil nutrient status in structuring tropical forest soil fungal communities.
Subject(s)
Ecosystem , Fungi/growth & development , Rain , Soil Microbiology , Soil/chemistry , Trees/classification , Tropical Climate , DNA, Fungal/analysis , DNA, Fungal/genetics , DNA, Fungal/isolation & purification , Fungi/classification , Fungi/genetics , Fungi/isolation & purification , Plant Leaves/metabolism , Plant Leaves/microbiology , Trees/microbiologyABSTRACT
Fungi influence nutrient cycling in terrestrial ecosystems, as they are major regulators of decomposition and soil respiration. However, little is known about the substrate preferences of individual fungal species outside of laboratory culture studies. If active fungi differ in their substrate preferences in situ, then changes in fungal diversity due to global change may dramatically influence nutrient cycling in ecosystems. To test the responses of individual fungal taxa to specific substrates, we used a nucleotide-analogue procedure in the boreal forest of Alaska (USA). Specifically, we added four organic N compounds commonly found in plant litter (arginine, glutamate, lignocellulose, and tannin-protein) to litterbags filled with decomposed leaf litter (black spruce and aspen) and assessed the responses of active fungal species using qPCR (quantitative polymerase chain reaction), oligonucleotide fingerprinting of rRNA genes, and sequencing. We also compared the sequences from our experiment with a concurrent warming experiment to see if active fungi that targeted more recalcitrant compounds would respond more positively to soil warming. We found that individual fungal taxa responded differently to substrate additions and that active fungal communities were different across litter types (spruce vs. aspen). Active fungi that targeted lignocellulose also responded positively to experimental warming. Additionally, resource-use patterns in different fungal taxa were genetically correlated, suggesting that it may be possible to predict the ecological function of active fungal communities based on genetic information. Together, these results imply that fungi are functionally diverse and that reductions in fungal diversity may have consequences for ecosystem functioning.
Subject(s)
Biodiversity , Fungi/classification , Fungi/physiology , DNA, Fungal/genetics , DNA, Ribosomal/genetics , Fungi/genetics , Temperature , Trees/physiologyABSTRACT
Bacteria and fungi drive the cycling of plant litter in forests, but little is known about their role in tropical rain forest nutrient cycling, despite the high rates of litter decay observed in these ecosystems. However, litter decay rates are not uniform across tropical rain forests. For example, decomposition can differ dramatically over small spatial scales between low-diversity, monodominant rain forests, and species-rich, mixed forests. Because the climatic patterns and soil parent material are identical in co-occurring mixed and monodominant forests, differences in forest floor accumulation, litter production, and decomposition between these forests may be biotically mediated. To test this hypothesis, we conducted field and laboratory studies in a monodominant rain forest in which the ectomycorrhizal tree Dicymbe corymbosa forms >80% of the canopy, and a diverse, mixed forest dominated by arbuscular mycorrhizal trees. After 2 years, decomposition was significantly slower in the monodominant forest (P < 0.001), but litter production was significantly greater in the mixed forest (P < 0.001). In the laboratory, we found microbial community biomass was greater in the mixed forest (P = 0.02), and the composition of fungal communities was distinct between the two rain forest types (P = 0.001). Sequencing of fungal rDNA revealed a significantly lower richness of saprotrophic fungi in the monodominant forest (19 species) relative to the species-rich forest (84 species); moreover, only 4% percent of fungal sequences occurred in both forests. These results show that nutrient cycling patterns in tropical forests can vary dramatically over small spatial scales, and that changes in microbial community structure likely drive the observed differences in decomposition.
Subject(s)
Ecosystem , Mycorrhizae/physiology , Soil Microbiology , Trees/microbiology , Tropical Climate , Biodiversity , Picea/microbiology , Trees/physiologyABSTRACT
Functional and biogeographical properties of soil microbial communities in urban ecosystems are poorly understood despite their role in metabolic processes underlying valuable ecosystem services. The worldwide emergence of engineered habitats in urban landscapes-green roofs, bioswales, and other types of soil-based green infrastructure-highlights the importance of understanding how environmental changes affect the community assembly processes that shape urban microbial diversity and function. In this study we investigated (1) whether engineered green roofs and bioswales in New York City had distinct microbial community composition and trait-associated diversity compared to non-engineered soils in parks and tree pits, and (2) if these patterns were consistent with divergent community assembly processes associated with engineered specifications of green infrastructure habitats not present in conventional, non-engineered green infrastructure; specifically, tree pit and park lawn soils. We found that green roofs and bioswales each had distinct bacterial and fungal communities, but that community composition and diversity were not significantly associated with geographic distance, suggesting that the processes structuring these differences are related to aspects of the habitats themselves. Bioswales, and to a lesser extent green roofs, also contained increased functional potential compared to conventional GI soils, based on the diversity and abundance of taxa associated with nitrogen cycling, biodegradation, decomposition, and traits positively associated with plant growth. We discuss these results in the context of community assembly theory, concluding that urban soil microbial community composition and diversity in engineered habitats are driven largely by environmental filtering, whereas stochastic processes are more important among non-engineered soils.
ABSTRACT
Bioswales and other forms of green infrastructure can be effective means to reduce environmental stresses in urban ecosystems; however, few studies have evaluated the ecology of these systems, or the role that plant selection and microbial assembly play in their function. For the current study, we examined the relationship between plant transpiration rates for five commonly planted herbaceous species in three bioswales in New York City, as well as bioswale soil microbial composition and soil chemistry. Soils were sampled near individual plants, with distinction made between upper (bioswale inlet) and lower slopes (bioswale outlet). We found high variation in transpiration rates across species, and that Nepeta × faassenii was the highest conductor (13.65 mmol H2O m-2s-1), while Panicum virgatum was the lowest conductor (2.67 mmol H2O m-2s-1) (p < 0.001). There was significant variation in percent N of leaves and soil, which did not relate to the higher water conductance in bioswales. Significantly higher C, N, and water content on the high end of bioswale slopes suggest storm water run-off is mostly absorbed on the inlet side. Bacterial and fungal communities were significantly clustered by bioswale and by plant species within each bioswale implying there are micro-environmental controls on the soil microbial composition, and that plant composition matters for microbial assemblages within bioswales. Plants with higher transpiration rates were associated with greater fungal and bacterial diversity at the level of the bioswale and at scale of the individual plant, suggesting a possible link between plant physiological traits and soil microbial communities. These data suggest that the specific plant palette selected for planting bioswales can have deterministic effects on the surrounding microbial communities which may further influence functions such as transpiration and nutrient cycling. These results may have implications for bioswale management to improve urban water quality and reduce stress on sewage systems after storm events by revising plant species palette selection based on the functional consequences of plant-microbial associations in engineered green infrastructure.
ABSTRACT
The emergence of high-throughput DNA sequencing methods provides unprecedented opportunities to further unravel bacterial biodiversity and its worldwide role from human health to ecosystem functioning. However, despite the abundance of sequencing studies, combining data from multiple individual studies to address macroecological questions of bacterial diversity remains methodically challenging and plagued with biases. Here, using a machine-learning approach that accounts for differences among studies and complex interactions among taxa, we merge 30 independent bacterial data sets comprising 1,998 soil samples from 21 countries. Whereas previous meta-analysis efforts have focused on bacterial diversity measures or abundances of major taxa, we show that disparate amplicon sequence data can be combined at the taxonomy-based level to assess bacterial community structure. We find that rarer taxa are more important for structuring soil communities than abundant taxa, and that these rarer taxa are better predictors of community structure than environmental factors, which are often confounded across studies. We conclude that combining data from independent studies can be used to explore bacterial community dynamics, identify potential 'indicator' taxa with an important role in structuring communities, and propose hypotheses on the factors that shape bacterial biogeography that have been overlooked in the past.
Subject(s)
Bacteria/classification , Bacterial Physiological Phenomena , Ecology , Microbiota , Soil Microbiology , Bacteria/genetics , Biodiversity , DNA, Bacterial/genetics , Ecosystem , High-Throughput Nucleotide Sequencing , Machine Learning , Microbial Interactions , Phylogeny , RNA, Ribosomal, 16S/genetics , SoilABSTRACT
Most tropical rain forests contain diverse arrays of tree species that form arbuscular mycorrhizae. In contrast, the less common monodominant rain forests, in which one tree species comprises more than 50% of the canopy, frequently contain ectomycorrhizal (ECM) associates. In this study, I explored the potential for common ECM networks, created by aggregations of ECM trees, to enhance seedling survivorship near parent trees. I determined the benefit conferred by the common ECM network on seedling growth and survivorship of an ECM monodominant species in Guyana. Seedlings with access to an ECM network had greater growth (73% greater), leaf number (55% more), and survivorship (47% greater) than seedlings without such access, suggesting that the ECM network provides a survivorship advantage. A survey of wild seedlings showed positive distance-dependent distribution and survival with respect to conspecific adults. These experimental and survey results suggest that the negative distance-dependent mechanisms at the seedling stage thought to maintain tropical rain forest diversity are reversed for ECM seedlings, which experience positive feedbacks from the ECM network. These results may in part explain the local monodominance of an ECM tree species within the matrix of high-diversity, tropical rain forest.
Subject(s)
Biodiversity , Mycorrhizae/physiology , Seedlings/growth & development , Symbiosis , Trees/microbiology , Analysis of Variance , Guyana , Seedlings/microbiology , Species Specificity , Trees/growth & development , Tropical ClimateABSTRACT
Habitat fragmentation is widespread across ecosystems, detrimentally affecting biodiversity. Although most habitat fragmentation studies have been conducted on macroscopic organisms, microbial communities and fungal processes may also be threatened by fragmentation. This study investigated whether fragmentation, and the effects of fragmentation on plants, altered fungal diversity and function within a fragmented shrubland in southern California. Using fluorimetric techniques, we assayed enzymes from plant litter collected from fragments of varying sizes to investigate enzymatic responses to fragmentation. To isolate the effects of plant richness from those of fragment size on fungi, we deployed litter bags containing different levels of plant litter diversity into the largest fragment and incubated in the field for one year. Following field incubation, we determined litter mass loss and conducted molecular analyses of fungal communities. We found that leaf-litter enzyme activity declined in smaller habitat fragments with less diverse vegetation. Moreover, we detected greater litter mass loss in litter bags containing more diverse plant litter. Additionally, bags with greater plant litter diversity harbored greater numbers of fungal taxa. These findings suggest that both plant litter resources and fungal function may be affected by habitat fragmentation's constraints on plants, possibly because plant species differ chemically, and may thus decompose at different rates. Diverse plant assemblages may produce a greater variety of litter resources and provide more ecological niche space, which may support greater numbers of fungal taxa. Thus, reduced plant diversity may constrain both fungal taxa richness and decomposition in fragmented coastal shrublands. Altogether, our findings provide evidence that even fungi may be affected by human-driven habitat fragmentation via direct effects of fragmentation on plants. Our findings underscore the importance of restoring diverse vegetation communities within larger coastal sage scrub fragments and suggest that this may be an effective way to improve the functional capacity of degraded sites.
Subject(s)
Biodiversity , Ecosystem , Fungi/growth & development , Plants/microbiology , California , Cellulose/metabolism , Chitin/metabolism , Fungi/classification , Fungi/enzymology , Plants/classification , Plants/metabolismABSTRACT
The role that mycorrhizal fungal associations play in the assembly of long-lived tree communities is poorly understood, especially in tropical forests, which have the highest tree diversity of any ecosystem. The lowland tropical rain forests of Southeast Asia are characterized by high levels of species richness within the family Dipterocarpaceae, the entirety of which has been shown to form obligate ectomycorrhizal (ECM) fungal associations. Differences in ECM assembly between co-occurring species of dipterocarp have been suggested, but never tested in adult trees, as a mechanism for maintaining the coexistence of closely related tree species in this family. Testing this hypothesis has proven difficult because the assembly of both dipterocarps and their ECM associates co-varies with the same edaphic variables. In this study, we used high-throughput DNA sequencing of soils and Sanger sequencing of root tips to evaluate how ECM fungi were structured within and across a clay-sand soil nutrient ecotone in a mixed-dipterocarp rain forest in Malaysian Borneo. We compared assembly patterns of ECM fungi in bulk soil to ECM root tips collected from three ecologically distinct species of dipterocarp. This design allowed us to test whether ECM fungi are more strongly structured by soil type or host specificity. As with previous studies of ECM fungi on this plot, we observed that clay vs. sand soil type strongly structured both the bulk soil and root tip ECM fungal communities. However, we also observed significantly different ECM communities associated with two of the three dipterocarp species evaluated on this plot. These results suggest that ECM fungal assembly on these species is shaped by a combination of biotic and abiotic factors, and that the soil edaphic niche occupied by different dipterocarp species may be mediated by distinct ECM fungal assemblages.
ABSTRACT
The biological diversity and composition of microorganisms influences both human health outcomes and ecological processes; therefore, understanding the factors that influence microbial biodiversity is key to creating healthy, functional landscapes in which to live. In general, biological diversity is predicted to be limited by habitat size, which for green areas is often reduced in cities, and by chronic disturbance (stress). These hypotheses have not previously been tested in microbial systems in direct comparison to macroorganisms. Here we analyzed bacterial, fungal and ant communities in small road medians (average area 0.0008 km(2)) and larger parks (average area 0.64 km(2)) across Manhattan (NYC). Bacterial species richness was not significantly different between medians and parks, but community composition was significantly distinct. In contrast, ant communities differed both in composition and richness with fewer ant species in medians than parks. Fungi showed no significant variation in composition or richness but had few shared taxa between habitats or sites. The diversity and composition of microbes appears less sensitive to habitat patchiness or urban stress than those of macroorganisms. Microbes and their associated ecosystem services and functions may be more resilient to the negative effects of urbanization than has been previously appreciated.
Subject(s)
Bacteria/isolation & purification , Biodiversity , Environmental Microbiology , Fungi/isolation & purification , Bacteria/classification , Bacteria/genetics , Ecosystem , Fungi/classification , Fungi/genetics , Humans , Molecular Sequence Data , New York City , Parks, Recreational , Phylogeny , Stress, Physiological , Urban HealthABSTRACT
Tropical smallholder agriculture is undergoing rapid transformation in nutrient cycling pathways as international development efforts strongly promote greater use of mineral fertilizers to increase crop yields. These changes in nutrient availability may alter the composition of microbial communities with consequences for rates of biogeochemical processes that control nutrient losses to the environment. Ecological theory suggests that altered microbial diversity will strongly influence processes performed by relatively few microbial taxa, such as denitrification and hence nitrogen losses as nitrous oxide, a powerful greenhouse gas. Whether this theory helps predict nutrient losses from agriculture depends on the relative effects of microbial community change and increased nutrient availability on ecosystem processes. We find that mineral and organic nutrient addition to smallholder farms in Kenya alters the taxonomic and functional diversity of soil microbes. However, we find that the direct effects of farm management on both denitrification and carbon mineralization are greater than indirect effects through changes in the taxonomic and functional diversity of microbial communities. Changes in functional diversity are strongly coupled to changes in specific functional genes involved in denitrification, suggesting that it is the expression, rather than abundance, of key functional genes that can serve as an indicator of ecosystem process rates. Our results thus suggest that widely used broad summary statistics of microbial diversity based on DNA may be inappropriate for linking microbial communities to ecosystem processes in certain applied settings. Our results also raise doubts about the relative control of microbial composition compared to direct effects of management on nutrient losses in applied settings such as tropical agriculture.
Subject(s)
Betacoronavirus , Coronavirus Infections , Leadership , Pandemics , Pneumonia, Viral , COVID-19 , Humans , SARS-CoV-2 , ScienceABSTRACT
Fungi regulate key nutrient cycling processes in many forest ecosystems, but their diversity and distribution within and across ecosystems are poorly understood. Here, we examine the spatial distribution of fungi across a boreal and tropical ecosystem, focusing on ectomycorrhizal fungi. We analyzed fungal community composition across litter (organic horizons) and underlying soil horizons (0-20 cm) using 454 pyrosequencing and clone library sequencing. In both forests, we found significant clustering of fungal communities by site and soil horizons with analogous patterns detected by both sequencing technologies. Free-living saprotrophic fungi dominated the recently-shed leaf litter and ectomycorrhizal fungi dominated the underlying soil horizons. This vertical pattern of fungal segregation has also been found in temperate and European boreal forests, suggesting that these results apply broadly to ectomycorrhizal-dominated systems, including tropical rain forests. Since ectomycorrhizal and free-living saprotrophic fungi have different influences on soil carbon and nitrogen dynamics, information on the spatial distribution of these functional groups will improve our understanding of forest nutrient cycling.