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1.
New Phytol ; 231(6): 2319-2332, 2021 09.
Artículo en Inglés | MEDLINE | ID: mdl-34091913

RESUMEN

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.


Asunto(s)
Festuca , Micobioma , Demografía , Germinación , Poaceae , Semillas
2.
Proc Natl Acad Sci U S A ; 113(51): 14811-14816, 2016 12 20.
Artículo en Inglés | MEDLINE | ID: mdl-27911822

RESUMEN

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.


Asunto(s)
Bacterias/genética , Parques Recreativos , Microbiología del Suelo , Suelo/química , Biodiversidad , Productos Biológicos , Diseño de Fármacos , Metagenoma , Microbiota , Ciudad de Nueva York , Filogenia , Análisis de Secuencia de ADN
3.
Ecology ; 99(3): 607-620, 2018 03.
Artículo en Inglés | MEDLINE | ID: mdl-29281752

RESUMEN

Arbuscular mycorrhizal (AM) fungi in the soil may influence tropical tree dynamics and forest succession. The mechanisms are poorly understood, because the functional characteristics and abundances of tree species and AM fungi are likely to be codependent. We used generalized joint attribute modeling to evaluate if AM fungi are associated with three forest community metrics for a sub-tropical montane forest in Puerto Rico. The metrics chosen to reflect changes during forest succession are the abundance of seedlings of different successional status, the amount of foliar damage on seedlings of different successional status, and community-weighted mean functional trait values (adult specific leaf area [SLA], adult wood density, and seed mass). We used high-throughput DNA sequencing to identify fungal operational taxonomic units (OTUs) in the soil. Model predictions showed that seedlings of mid- and late-successional species had less leaf damage when the 12 most common AM fungi were abundant compared to when these fungi were absent. We also found that seedlings of mid-successional species were predicted to be more abundant when the 12 most common AM fungi were abundant compared to when these fungi were absent. In contrast, early-successional tree seedlings were predicted to be less abundant when the 12 most common AM fungi were abundant compared to when these fungi were absent. Finally, we showed that, among the 12 most common AM fungi, different AM fungi were correlated with functional trait characteristics of early- or late-successional species. Together, these results suggest that early-successional species might not rely as much as mid- and late-successional species on AM fungi, and AM fungi might accelerate forest succession.


Asunto(s)
Micorrizas/genética , Hongos , Puerto Rico , Plantones/microbiología , Microbiología del Suelo , Árboles/microbiología
4.
Appl Environ Microbiol ; 83(16)2017 08 15.
Artículo en Inglés | MEDLINE | ID: mdl-28576763

RESUMEN

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.


Asunto(s)
Bacterias/aislamiento & purificación , Filogenia , Microbiología del Suelo , Bacterias/clasificación , Bacterias/genética , Bacterias/metabolismo , Biodiversidad , ADN Bacteriano/genética , Hidrocarburos/metabolismo , Ciudad de Nueva York , ARN Bacteriano/genética , ARN Ribosómico 16S/genética , Remodelación Urbana
5.
Ecology ; 98(3): 712-720, 2017 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-27984646

RESUMEN

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.


Asunto(s)
Bosques , Micorrizas/clasificación , Plantones/microbiología , Microbiología del Suelo , Árboles/microbiología , Biodiversidad , Micorrizas/fisiología , Puerto Rico
6.
J Eukaryot Microbiol ; 63(3): 363-6, 2016 05.
Artículo en Inglés | MEDLINE | ID: mdl-26662659

RESUMEN

Global warming significantly affects Arctic tundra, including permafrost thaw and soluble C release that may differentially affect tundra microbial growth. Using laboratory experiments, we report some of the first evidence for the effects of soluble glucose-C enrichment on tundra soil prokaryotes (bacteria and archaea) and fungi, with comparisons to microbial eukaryotes. Fungal increase in C-biomass was equivalent to 10% (w/w) of the added glucose-C, and for prokaryote biomass 2% (w/w), the latter comparable to prior published results. The C-gain after 14 d was 1.3 mg/g soil for fungi, and ~200 µg/g for prokaryotes.


Asunto(s)
Carbono/metabolismo , Hongos/crecimiento & desarrollo , Hongos/aislamiento & purificación , Microbiología del Suelo , Tundra , Archaea/metabolismo , Bacterias/metabolismo , Biomasa , Ecosistema , Eucariontes/metabolismo , Hongos/clasificación , Hongos/genética , Calentamiento Global , Glucosa/metabolismo , Sphagnopsida
7.
Ecol Appl ; 26(6): 1881-1895, 2016 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-27755697

RESUMEN

Our understanding of the long-lasting effects of human land use on soil fungal communities in tropical forests is limited. Yet, over 70% of all remaining tropical forests are growing in former agricultural or logged areas. We investigated the relationship among land use history, biotic and abiotic factors, and soil fungal community composition and diversity in a second-growth tropical forest in Puerto Rico. We coupled high-throughput DNA sequencing with tree community and environmental data to determine whether land use history had an effect on soil fungal community descriptors. We also investigated the biotic and abiotic factors that underlie such differences and asked whether the relative importance of biotic (tree diversity, basal tree area, and litterfall biomass) and abiotic (soil type, pH, iron, and total carbon, water flow, and canopy openness) factors in structuring soil fungal communities differed according to land use history. We demonstrated long-lasting effects of land use history on soil fungal communities. At our research site, most of the explained variation in soil fungal composition (R2  = 18.6%), richness (R2  = 11.4%), and evenness (R2  = 10%) was associated with edaphic factors. Areas previously subject to both logging and farming had a soil fungal community with lower beta diversity and greater evenness of fungal operational taxonomic units (OTUs) than areas subject to light logging. Yet, fungal richness was similar between the two areas of historical land use. Together, these results suggest that fungal communities in disturbed areas are more homogeneous and diverse than in areas subject to light logging. Edaphic factors were the most strongly correlated with soil fungal composition, especially in areas subject to light logging, where soils are more heterogenous. High functional tree diversity in areas subject to both logging and farming led to stronger correlations between biotic factors and fungal composition than in areas subject to light logging. In contrast, fungal richness and evenness were more strongly correlated with biotic factors in areas of light logging, suggesting that these metrics might reflect long-term associations in old-growth forests. The large amount of unexplained variance in fungal composition suggests that these communities are structured by both stochastic and niche assemblage processes.


Asunto(s)
Hongos/clasificación , Hongos/fisiología , Bosque Lluvioso , Microbiología del Suelo , Puerto Rico , Factores de Tiempo , Clima Tropical
8.
Ecol Lett ; 18(8): 807-816, 2015 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-26032408

RESUMEN

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.


Asunto(s)
Micorrizas/clasificación , Microbiología del Suelo , Simbiosis , Árboles/microbiología , Borneo , ADN de Hongos/genética , Hongos/clasificación , Hongos/genética , Modelos Lineales , Micorrizas/genética , Raíces de Plantas/microbiología , Bosque Lluvioso , Análisis de Secuencia de ADN , Suelo , Árboles/clasificación , Clima Tropical
9.
Ecol Lett ; 18(12): 1397-405, 2015 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-26472095

RESUMEN

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.


Asunto(s)
Fenómenos Fisiológicos Bacterianos , Biodiversidad , Hongos/fisiología , Microbiología del Suelo , Árboles/fisiología , Microbiota , Panamá , Raíces de Plantas/fisiología , Bosque Lluvioso , Clima Tropical
10.
Ecol Lett ; 17(9): 1086-93, 2014 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-24912000

RESUMEN

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.


Asunto(s)
Evolución Biológica , Hongos/fisiología , Microbiología del Suelo , Biodiversidad , Ecosistema , Hongos/clasificación , Hongos/genética , Filogenia , ARN Ribosómico 18S/genética , Clima Tropical
11.
Commun Biol ; 6(1): 1066, 2023 10 19.
Artículo en Inglés | MEDLINE | ID: mdl-37857800

RESUMEN

One mechanism proposed to explain high species diversity in tropical systems is strong negative conspecific density dependence (CDD), which reduces recruitment of juveniles in proximity to conspecific adult plants. Although evidence shows that plant-specific soil pathogens can drive negative CDD, trees also form key mutualisms with mycorrhizal fungi, which may counteract these effects. Across 43 large-scale forest plots worldwide, we tested whether ectomycorrhizal tree species exhibit weaker negative CDD than arbuscular mycorrhizal tree species. We further tested for conmycorrhizal density dependence (CMDD) to test for benefit from shared mutualists. We found that the strength of CDD varies systematically with mycorrhizal type, with ectomycorrhizal tree species exhibiting higher sapling densities with increasing adult densities than arbuscular mycorrhizal tree species. Moreover, we found evidence of positive CMDD for tree species of both mycorrhizal types. Collectively, these findings indicate that mycorrhizal interactions likely play a foundational role in global forest diversity patterns and structure.


Asunto(s)
Micorrizas , Retroalimentación , Simbiosis , Plantas/microbiología , Suelo
12.
Microb Ecol ; 63(4): 804-12, 2012 May.
Artículo en Inglés | MEDLINE | ID: mdl-22080256

RESUMEN

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.


Asunto(s)
Ecosistema , Hongos/crecimiento & desarrollo , Lluvia , Microbiología del Suelo , Suelo/química , Árboles/clasificación , Clima Tropical , ADN de Hongos/análisis , ADN de Hongos/genética , ADN de Hongos/aislamiento & purificación , Hongos/clasificación , Hongos/genética , Hongos/aislamiento & purificación , Hojas de la Planta/metabolismo , Hojas de la Planta/microbiología , Árboles/microbiología
13.
Ecology ; 91(8): 2324-32, 2010 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-20836454

RESUMEN

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.


Asunto(s)
Biodiversidad , Hongos/clasificación , Hongos/fisiología , ADN de Hongos/genética , ADN Ribosómico/genética , Hongos/genética , Temperatura , Árboles/fisiología
14.
Oecologia ; 164(3): 785-95, 2010 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-20577764

RESUMEN

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.


Asunto(s)
Ecosistema , Micorrizas/fisiología , Microbiología del Suelo , Árboles/microbiología , Clima Tropical , Biodiversidad , Picea/microbiología , Árboles/fisiología
15.
FEMS Microbiol Ecol ; 96(9)2020 09 01.
Artículo en Inglés | MEDLINE | ID: mdl-32789510

RESUMEN

Soil microbes are essential to the continued productivity of sustainably managed agroecosystems. In shade coffee plantations, the relationship between soil microbial composition, soil nutrient availability and coffee productivity have been demonstrated, but the effects of management on the composition of the soil microbial communities remains relatively unexplored. To further understand how management modulates the soil microbiome, the soil fungal and bacterial communities, soil chemistry, and canopy composition were surveyed in a Nicaraguan coffee cooperative, across 19 individual farms. Amplicon sequencing analyses showed that management (organic or conventional), stand age and previous land use affected the soil microbiome, albeit in different ways. Bacterial communities were most strongly associated with soil chemistry, while fungal communities were more strongly associated with the composition of the canopy and historical land use of the coffee plantation. Notably, both fungal and bacterial richness decreased with stand age. In addition to revealing the first in-depth characterization of the soil microbiome in coffee plantations in Nicaragua, these results highlight how fungal and bacterial communities are simultaneously modulated by long-term land use legacies (i.e. an agricultural plot's previous land use) and short-term press disturbance (i.e. farm age).


Asunto(s)
Micobioma , Suelo , Agricultura , Café , Hongos/genética , Microbiología del Suelo
16.
mBio ; 11(5)2020 10 27.
Artículo en Inglés | MEDLINE | ID: mdl-33109755

RESUMEN

Phosphorus (P) is an essential nutrient that is often in limited supply, with P availability constraining biomass production in many terrestrial ecosystems. Despite decades of work on plant responses to P deficiency and the importance of soil microbes to terrestrial ecosystem processes, how soil microbes respond to, and cope with, P deficiencies remains poorly understood. We studied 583 soils from two independent sample sets that each span broad natural gradients in extractable soil P and collectively represent diverse biomes, including tropical forests, temperate grasslands, and arid shrublands. We paired marker gene and shotgun metagenomic analyses to determine how soil bacterial and archaeal communities respond to differences in soil P availability and to detect corresponding shifts in functional attributes. We identified microbial taxa that are consistently responsive to extractable soil P, with those taxa found in low P soils being more likely to have traits typical of oligotrophic life history strategies. Using environmental niche modeling of genes and gene pathways, we found an enriched abundance of key genes in low P soils linked to the carbon-phosphorus (C-P) lyase and phosphonotase degradation pathways, along with key components of the high-affinity phosphate-specific transporter (Pst) and phosphate regulon (Pho) systems. Taken together, these analyses suggest that catabolism of phosphonates is an important strategy used by bacteria to scavenge phosphate in P-limited soils. Surprisingly, these same pathways are important for bacterial growth in P-limited marine waters, highlighting the shared metabolic strategies used by both terrestrial and marine microbes to cope with P limitation.


Asunto(s)
Bacterias/metabolismo , Fósforo/metabolismo , Microbiología del Suelo , Bacterias/clasificación , Ecosistema , Bosques , Metagenoma , Metagenómica , Consorcios Microbianos , Nitrógeno/metabolismo
17.
Front Microbiol ; 11: 912, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-32582043

RESUMEN

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.

18.
Front Microbiol ; 10: 2368, 2019.
Artículo en Inglés | MEDLINE | ID: mdl-31824435

RESUMEN

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.

19.
Nat Microbiol ; 3(2): 189-196, 2018 02.
Artículo en Inglés | MEDLINE | ID: mdl-29158606

RESUMEN

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.


Asunto(s)
Bacterias/clasificación , Fenómenos Fisiológicos Bacterianos , Ecología , Microbiota , Microbiología del Suelo , Bacterias/genética , Biodiversidad , ADN Bacteriano/genética , Ecosistema , Secuenciación de Nucleótidos de Alto Rendimiento , Aprendizaje Automático , Interacciones Microbianas , Filogenia , ARN Ribosómico 16S/genética , Suelo
20.
Ecology ; 88(3): 567-74, 2007 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-17503583

RESUMEN

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.


Asunto(s)
Biodiversidad , Micorrizas/fisiología , Plantones/crecimiento & desarrollo , Simbiosis , Árboles/microbiología , Análisis de Varianza , Guyana , Plantones/microbiología , Especificidad de la Especie , Árboles/crecimiento & desarrollo , Clima Tropical
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