Pervasive and strong effects of plants on soil chemistry: a meta-analysis of individual plant 'Zinke' effects

A Spatial Signal of Niche Differentiation in Tropical Forests

AbstractExplaining diversity in tropical forests remains a challenge in community ecology. Theory tells us that species differences can stabilize communities by reducing competition, while species similarities can promote diversity by reducing fitness differences and thus prolonging the time to competitive exclusion. Combined, these processes may lead to clustering of species such that species are niche differentiated across clusters and share a niche within each cluster. Here, we characterize this partial niche differentiation in a tropical forest in Panama by measuring spatial clustering of woody plants and relating these clusters to local soil conditions. We find that species were spatially clustered and the clusters were associated with specific concentrations of soil nutrients, reflecting the existence of nutrient niches. Species were almost twice as likely to recruit in their own nutrient niche. A decision tree algorithm showed that local soil conditions correctly predicted the niche of the trees with up to 85% accuracy. Iron, zinc, phosphorus, manganese, and soil pH were among the best predictors of species clusters.

Four Invasive Plant Species in Southwest Saudi Arabia Have Variable Effects on Soil Dynamics

Predicting the direction and magnitude of change in soil dynamics caused by invasive plant species has proven to be difficult because these changes are often reported to be species- and habitat-specific. This study was conducted to determine changes in three soil properties, eight soil ions, and seven soil microelements under established stands of four invasive plants, Prosopis juliflora, Ipomoea carnea, Leucaena leucocephala, and Opuntia ficus-indica. Soil properties, ions, and microelements were measured in sites invaded by these four species in southwest Saudi Arabia, and these values were compared to the results for the same 18 parameters from adjacent sites with native vegetation. Because this study was conducted in an arid ecosystem, we predict that these four invasive plants will significantly alter the soil properties, ions, and microelements in the areas they invaded. While the soils of sites with the four invasive plant species generally had higher values for soil properties and ions compared to sites with native vegetation, in most instances these differences were not statistically significant. However, the soils within sites invaded by I. carnea, L. leucocephala, and P. juliflora had statistically significant differences for some soil parameters. For sites invaded by O. puntia ficus-indica, no soil properties, ions, or microelements were significantly different compared to adjacent sites with native vegetation. Sites invaded by the four plant species generally exhibited differences in the 11 soil properties, but in no instance were these differences statistically significant. All three soil properties and one soil ion (Ca) were significantly different across the four stands of native vegetation. For the seven soil microelements, significantly different values were detected for Co and Ni, but only among stands of the four invasive plant species. These results indicate that the four invasive plant species altered soil properties, ions, and microelements, but for most of the parameters we assessed, not significantly. Our results do not support our initial prediction, but are in general agreement with previous published findings, which indicate that the effects of invasive plants on soil dynamics vary idiosyncratically among invasive species and among invaded habitats.

Plant and fungal species interactions differ between aboveground and belowground habitats in mountain forests of eastern China

Plant and fungal species interactions drive many essential ecosystem properties and processes; however, how these interactions differ between aboveground and belowground habitats remains unclear at large spatial scales. Here, we surveyed 494 pairwise fungal communities in leaves and soils by Illumina sequencing, which were associated with 55 woody plant species across more than 2,000-km span of mountain forests in eastern China. The relative contributions of plant, climate, soil and space to the variation of fungal communities were assessed, and the plant-fungus network topologies were inferred. Plant phylogeny was the strongest predictor for fungal community composition in leaves, accounting for 19.1% of the variation. In soils, plant phylogeny, climatic factors and soil properties explained 9.2%, 9.0% and 8.7% of the variation in soil fungal community, respectively. The plant-fungus networks in leaves exhibited significantly higher specialization, modularity and robustness (resistance to node loss), but less complicated topology (e.g., significantly lower linkage density and mean number of links) than those in soils. In addition, host/fungus preference combinations and key species, such as hubs and connectors, in bipartite networks differed strikingly between aboveground and belowground samples. The findings provide novel insights into cross-kingdom (plant-fungus) species co-occurrence at large spatial scales. The data further suggest that community shifts of trees due to climate change or human activities will impair aboveground and belowground forest fungal diversity in different ways.

Contrasts among cationic phytochemical landscapes in the southern United States

Understanding the phytochemical landscapes of essential and nonessential chemical elements to plants provides an opportunity to better link biogeochemical cycles to trophic ecology. We investigated the formation and regulation of the cationic phytochemical landscapes of four key elements for biota: Ca, Mg, K, and Na. We collected aboveground tissues of plants in Atriplex, Helianthus, and Opuntia and adjacent soils from 51, 131, and 83 sites, respectively, across the southern United States. We determined the spatial variability of these cations in plants and soils. Also, we quantified the homeostasis coefficient for each cation and genus combination, by using mixed-effect models, with spatially correlated random effects. Additionally, using random forest models, we modeled the influence of bioclimatic, soil, and spatial variables on plant cationic concentrations. Sodium variability and spatial autocorrelation were considerably greater than for Ca, Mg, or K. Calcium, Mg, and K exhibited strongly homeostatic patterns, in striking contrast to non-homeostatic Na. Even so, climatic and soil variables explained a large proportion of plants' cationic concentrations. Essential elements (Ca, Mg, and K) appeared to be homeostatically regulated, which contrasted sharply with Na, a nonessential element for most plants. In addition, we provide evidence for the No-Escape-from-Sodium hypothesis in real-world ecosystems, indicating that plant Na concentrations tend to increase as substrate Na levels increase.

Can the impact of canopy trees on soil and understory be altered using litter additions?

Trees can have large effects on soil nutrients in ways that alter succession, particularly in the case of nitrogen-(N)-fixing trees. In Hawai'i, forest restoration relies heavily on use of a native N-fixing tree, Acacia koa (koa), but this species increases soil-available N and likely facilitates competitive dominance of exotic pasture grasses. In contrast, Metrosideros polymorpha ('ōhi'a), the dominant native tree in Hawai'i, is less often planted because it is slow growing; yet it is typically associated with lower soil N and grass biomass, and greater native understory recruitment. We experimentally tested whether it is possible to reverse high soil N under koa by adding 'ōhi'a litter, using additions of koa litter or no litter as controls, over 2.5 yr. We then quantified natural litterfall and decomposition rates of 'ōhi'a and koa litter to place litter additions in perspective. Finally, we quantified whether litter additions altered grass biomass and if this had effects on native outplants. Adding 'ōhi'a litter increased soil carbon, but increased rather than decreased inorganic soil N pools. Contrary to expectations, koa litter decomposed more slowly than 'ōhi'a, although it released more N per unit of litter. We saw no reduction in grass biomass due to 'ōhi'a litter addition, and no change in native outplanted understory survival or growth. We conclude that the high N soil conditions under koa are difficult to reverse. However, we also found that outplanted native woody species were able to decrease exotic grass biomass over time, regardless of the litter environment, making this a better strategy for lowering exotic species impacts.

Plant biodiversity and the regeneration of soil fertility

Fertile soils have been an essential resource for humanity for 10,000 y, but the ecological mechanisms involved in the creation and restoration of fertile soils, and especially the role of plant diversity, are poorly understood. Here we use results of a long-term, unfertilized plant biodiversity experiment to determine whether biodiversity, especially plant functional biodiversity, impacted the regeneration of fertility on a degraded sandy soil. After 23 y, plots containing 16 perennial grassland plant species had, relative to monocultures of these same species, ∼30 to 90% greater increases in soil nitrogen, potassium, calcium, magnesium, cation exchange capacity, and carbon and had ∼150 to 370% greater amounts of N, K, Ca, and Mg in plant biomass. Our results suggest that biodiversity, likely in combination with the increased plant productivity caused by higher biodiversity, led to greater soil fertility. Moreover, plots with high plant functional diversity, those containing grasses, legumes, and forbs, accumulated significantly greater N, K, Ca, and Mg in the total nutrient pool (plant biomass and soil) than did plots containing just one of these three functional groups. Plant species in these functional groups had trade-offs between their tissue N content, tissue K content, and root mass, suggesting why species from all three functional groups were essential for regenerating soil fertility. Our findings suggest that efforts to regenerate soil C stores and soil fertility may be aided by creative uses of plant diversity.

Novel chemicals engender myriad invasion mechanisms

Non-native invasive species (NIS) release chemicals into the environment that are unique to the invaded communities, defined as novel chemicals. Novel chemicals impact competitors, soil microbial communities, mutualists, plant enemies, and soil nutrients differently than in the species' native range. Ecological functions of novel chemicals and differences in functions between the native and non-native ranges of NIS are of immense interest to ecologists. Novel chemicals can mediate different ecological, physiological, and evolutionary mechanisms underlying invasion hypotheses. Interactions amongst the NIS and resident species including competitors, soil microbes, and plant enemies, as well as abiotic factors in the invaded community are linked to novel chemicals. However, we poorly understand how these interactions might enhance NIS performance. New empirical data and analyses of how novel chemicals act in the invaded community will fill major gaps in our understanding of the chemistry of biological invasions. A novel chemical-invasion mechanism framework shows how novel chemicals engender invasion mechanisms beyond plant-plant or plant-microorganism interactions.

Natural soil microbiome variation affects spring foliar phenology with consequences for plant productivity and climate-driven range shifts

Identifying the potential for natural soil microbial communities to predictably affect complex plant traits is an important frontier in climate change research. Plant phenology varies with environmental and genetic factors, but few studies have examined whether the soil microbiome interacts with plant population differentiation to affect phenology and ecosystem function. We compared soil microbial variation in a widespread tree species (Populus angustifolia) with different soil inoculum treatments in a common garden environment to test how the soil microbiome affects spring foliar phenology and subsequent biomass growth. We hypothesized and show that soil bacterial and fungal communities vary with tree conditioning from different populations and elevations, that this soil community variation influences patterns of foliar phenology and plant growth across populations and elevation gradients, and that transferring lower elevation plant genotypes to higher elevation soil communities delayed foliar phenology, thereby shortening the growing season and reducing annual biomass production. Our findings show the importance of plant-soil interactions that help shape the timing of tree foliar phenology and productivity. These geographic patterns in plant population × microbiome interactions also broaden our understanding of how soil communities impact plant phenotypic variation across key climate change gradients, with consequences for ecosystem functioning.

Aboveground and Belowground Plant Traits Explain Latitudinal Patterns in Topsoil Fungal Communities From Tropical to Cold Temperate Forests

Soil fungi predominate the forest topsoil microbial biomass and participate in biogeochemical cycling as decomposers, symbionts, and pathogens. They are intimately associated with plants but their interactions with aboveground and belowground plant traits are unclear. Here, we evaluated soil fungal communities and their relationships with leaf and root traits in nine forest ecosystems ranging from tropical to cold temperate along a 3,700-km transect in eastern China. Basidiomycota was the most abundant phylum, followed by Ascomycota, Zygomycota, Glomeromycota, and Chytridiomycota. There was no latitudinal trend in total, saprotrophic, and pathotrophic fungal richness. However, ectomycorrhizal fungal abundance and richness increased with latitude significantly and reached maxima in temperate forests. Saprotrophic and pathotrophic fungi were most abundant in tropical and subtropical forests and their abundance decreased with latitude. Spatial and climatic factors, soil properties, and plant traits collectively explained 45% of the variance in soil fungal richness. Specific root length and root biomass had the greatest direct effects on total fungal richness. Specific root length was the key determinant of saprotrophic and pathotrophic fungal richness while root phosphorus content was the main biotic factor determining ectomycorrhizal fungal richness. In contrast, spatial and climatic features, soil properties, total leaf nitrogen and phosphorus, specific root length, and root biomass collectively explained >60% of the variance in fungal community composition. Soil fungal richness and composition are strongly controlled by both aboveground and belowground plant traits. The findings of this study provide new evidence that plant traits predict soil fungal diversity distribution at the continental scale.

Short-lived legacies of Prunus serotina plant-soil feedbacks

Plant-soil feedbacks (PSFs) are often involved in fundamental ecological processes such as plant succession and species coexistence. After a plant initiating PSFs dies, legacies of PSFs occurring as soil signatures that influence subsequent plants could persist for an unknown duration. Altered resource environments following plant death (especially light availability) could affect whether legacy effects manifest and persist. To evaluate PSFs and their legacies, we obtained soils from a chronosequence of Prunus serotina harvests. In a greenhouse experiment, we planted conspecific seedlings under two light levels in these soils of varying time since the influence of live Prunus serotina, and compared seed/seedling survival in soils from live trees, stumps, and surrounding forest matrix within each site and across the chronosequence. PSF legacies were measured as the difference between seedling performance in live tree and stump soils within a site. Negative PSF legacies of P. serotina were short-lived, lasting up to 0.5 years after tree removal. These effects occurred under 5% but not 30% full sun. PSFs and their legacies manifested in seed/seedling survival, but not biomass. Though restricted to low light, short-lived legacies of P. serotina PSFs could have lasting impacts on plant community dynamics during post-disturbance regeneration by disfavoring P. serotina regeneration in small tree-fall gaps.

Changes in Soil Features and Phytomass during Vegetation Succession in Sandy Areas

This research was conducted on an area of inland sands characterised by various degrees of overgrowth by vegetation and soil stabilisation. This landscape’s origin is not natural but is connected to human industrial activities dating from early medieval times, which created a powerful centre for mining and metallurgy. This study aims to identify the changes in the above- and belowground phytomass in the initial stages of succession and their influence on the chemical properties and morphology of the soil. It was found that Salix arenaria dominated in primary phytomass production in all plots tested. The amounts of this species found in each community were as follows: 8.55 kg/400 m2 (algae–mosses), 188.97 kg/400 m2 (sand grassland–willow), 123.44 kg/400 m2 (pine–willow–mosses), 14.63 kg/400 m2 (sand grassland–mosses–willow), and 196.55 kg/400 m2 (willow–pine–sand grassland). A notable share of Koeleria glauca was found in the phytomass production of Plots IV (45.73 kg) and V (86.16 kg). Basic soil properties (pH, Corg, Nt), available plant elements (P), and plant nutrients (Ca, Mg, K, P, Fe) beneath the dominant plant species were examined. Soil acidity (pH) varied greatly, ranging from acidic (pH = 3.2) to weakly acidic (pH = 6.3). The content of organic carbon (Corg) in individual plots beneath the dominant species in the humus horizon ranged from 0.28% to 1.42%. The maximum contents of organic carbon and total nitrogen were found in organic (O) and organic-humus (OA) horizons. The highest Pavail content was found in organic and organic-humus horizons, ranging from 10.41 to 65.23 mg/kg, and in mineral horizons under K. glauca (24.10 mg/kg) and Salix acutifola (25.11 mg/kg). The soil features and phytomass were varied differently across individual sites, representing different stages of succession.

Patterns and mechanisms of spatial variation in tropical forest productivity, woody residence time, and biomass

Tropical forests vary widely in biomass carbon (C) stocks and fluxes even after controlling for forest age. A mechanistic understanding of this variation is critical to accurately predicting responses to global change. We review empirical studies of spatial variation in tropical forest biomass, productivity and woody residence time, focusing on mature forests. Woody productivity and biomass decrease from wet to dry forests and with elevation. Within lowland forests, productivity and biomass increase with temperature in wet forests, but decrease with temperature where water becomes limiting. Woody productivity increases with soil fertility, whereas residence time decreases, and biomass responses are variable, consistent with an overall unimodal relationship. Areas with higher disturbance rates and intensities have lower woody residence time and biomass. These environmental gradients all involve both direct effects of changing environments on forest C fluxes and shifts in functional composition - including changing abundances of lianas - that substantially mitigate or exacerbate direct effects. Biogeographic realms differ significantly and importantly in productivity and biomass, even after controlling for climate and biogeochemistry, further demonstrating the importance of plant species composition. Capturing these patterns in global vegetation models requires better mechanistic representation of water and nutrient limitation, plant compositional shifts and tree mortality.

Tree Species Richness and Neighborhood Effects on Ectomycorrhizal Fungal Richness and Community Structure in Boreal Forest

Tree species identity is one of the key factors driving ectomycorrhizal (EcM) fungal richness and community composition in boreal and temperate forest ecosystems, but little is known about the influence of tree species combinations and their neighborhood effects on EcM communities. To advance our understanding of host plant effects on EcM fungi, the roots of silver birch, Scots pine, and Norway spruce were analyzed using high-throughput sequencing across mature boreal forest exploratory plots of monocultures and two- and three-species mixtures in Finland. Our analyses revealed that tree species identity was an important determinant of EcM fungal community composition, but tree species richness had no significant influence on EcM fungal richness and community composition. We found that EcM fungal community composition associated with spruce depends on neighboring tree species. Our study suggests that at a regional-scale tree species identity is the primary factor determining community composition of root-associated EcM fungi alongside with tree species composition effects on EcM fungal community of spruce in mixed stands.

The role of the locoweed (Astragalus variabilis Bunge) in improving the soil properties of desert grasslands

Astragalus variabilis Bunge is a widespread locoweed that threatens livestock production in desert grassland. No research has reported its possible ecological functions due to focus being on its negative effect on livestock production. This study aimed to assess the effects of A. variabilis on soil properties and its possible role in improving soil quality in desert grassland. Soil samples were collected in Astragalus patches and the adjacent bare patches over two successive growing seasons in Alxa desert grassland where A. variabilis was favoured to spread. Soil properties including texture, water content, dry bulk density, porosity, available nutrients, organic matter, and soil microbial biomass were determined at 15 study sites. There was no significant difference in soil texture between Astragalus-dominant and bare patches; but organic matter (OM), available N and P, and microbial biomass in surface soil (0–30cm) were significantly higher in Astragalus patches. Furthermore, microbial biomass showed a significantly positive correlation with available nutrients and OM. Levels of water soluble salt were significantly lower in A. variabilis surface soils under drought conditions. Results suggested that A. variabilis was associated with some positive changes in soil properties, and was potentially important in improving soil chemical and microbial properties in desert grassland ecosystems. Consequently, total elimination of locoweed should not necessarily be considered the best solution to locoweed poisoning in livestock.

Contrasting fungal responses to wildfire across different ecosystem types

Wildfire affects our planet's biogeochemistry both by burning biomass and by driving changes in ecological communities and landcover. Some plants and ecosystem types are threatened by increasing fire pressure while others respond positively to fire, growing in local and regional abundance when it occurs regularly. However, quantifying total ecosystem response to fire demands consideration of impacts not only on aboveground vegetation, but also on soil microbes like fungi, which influence decomposition and nutrient mineralization. If fire-resistant soil fungal communities co-occur with similarly adapted plants, these above- and belowground ecosystem components should shift and recover in relative synchrony after burning. If not, fire might decouple ecosystem processes governed by these different communities, affecting total functioning. Here, we use a natural experiment to test whether fire-dependent ecosystems host unique, fire-resistant fungal communities. We surveyed burned and unburned areas across two California ecosystem types with differing fire ecologies in the immediate aftermath of a wildfire, finding that the soil fungal communities of fire-dependent oak woodlands differ from those of neighbouring mixed evergreen forests. We discovered furthermore that the latter are more strongly altered compositionally by fire than the former, suggesting that differences in fungal community structure support divergent community responses to fire across ecosystems. Our results thus indicate that fire-dependent ecosystems may host fire-resistant fungal communities.

Plant nutrient-acquisition strategies drive topsoil microbiome structure and function

Plant nutrient-acquisition strategies drive soil processes and vegetation performance, but their effect on the soil microbiome remains poorly understood. This knowledge is important to predict the shifts in microbial diversity and functions due to increasing changes in vegetation traits under global change. Here we documented the topsoil microbiomes of 145 boreal and temperate terrestrial sites in the Baltic region that broadly differed in vegetation type and nutritional traits, such as mycorrhizal types and symbiotic nitrogen-fixation. We found that sites dominated by arbuscular mycorrhizal (AM) vegetation harbor relatively more AM fungi, bacteria, fungal saprotrophs, and pathogens in the topsoil compared with sites dominated by ectomycorrhizal (EM) plants. These differences in microbiome composition reflect the rapid nutrient cycling and negative plant-soil feedback in AM soils. Lower fungal diversity and bacteria : fungi ratios in EM-dominated habitats are driven by monodominance of woody vegetation as well as soil acidification by EM fungi, which are associated with greater diversity and relative abundance of carbohydrate-active enzymes. Our study suggests that shifts in vegetation related to global change and land use may strongly alter the topsoil microbiome structure and function.

Recognizing the role of plant species composition in the modification of soil nutrients and water in rubber agroforestry systems

Reliable guidance for crop selection and related management to achieve sustainable soil resource use in rubber agroforestry systems is limited. One important reason for this limited guidance is that our understanding of the effects of different plant functional groups on soil resources is still insufficient. Here, to examine the effects of the species composition of trees, shrubs and herbs on soil nutrients and soil water with increases in the complexity of the plant community structure, we measured the soil nutrient concentrations (i.e., C, N, P, K, Ca and Mg), soil water content and soil water residence time (with stable hydrogen and oxygen isotope tracers) at six soil depths in a monoculture rubber plantation, four multi-species rubber agroforestry systems, and a tropical rainforest. As the plant species composition increased, the soil C and N increased. The soil water content also increased with increases in soil C and N. However, the effects of plant species composition on the soil water content gradually changed from positive to negative, especially under the effects of herb species, which could accelerate soil water drainage and hence shorten the soil water residence time. Therefore, the faster water infiltration and potentially higher flow of soil water in complex plant communities increased the risk and magnitude of mineral nutrient leaching. In addition, as the plant composition increased, plant competition decreased the concentration of soil nutrients, especially soil P, K and Ca. In general, plant interspecific interactions definitively decreased soil mineral nutrients as the plant composition increased, and the effects of tree, shrub and herb species on soil nutrients and soil water differed and sometimes appeared contradictory. However, the effects of plant species composition on soil gradually weakened with increases in soil depth.

Fertility-related interplay between fungal guilds underlies plant richness-productivity relationships in natural grasslands

The plant richness-productivity relationship is a central subject in ecology, yet the mechanisms behind this pattern remain debated. Soil fungi are closely associated with the dynamics of plant communities, however empirical evidence on how fungal communities integrate into the richness-productivity relationships of natural environments is lacking. We used Illumina high-throughput sequencing to identify rhizosphere fungal communities across a natural plant richness gradient at two sites with different fertility conditions, and related the subsequent information to plant richness and productivity to elucidate the role of fungal guilds in integrating the linkages of both plant components. Saprotrophs, mycorrhizal fungi and potential plant pathogens interacted differently between the sites, with saprotrophic and mycorrhizal fungal abundances being positively correlated at the high-nutrient site and abundances of mycorrhizal fungi and potential plant pathogens being negatively correlated at the low-nutrient site. The synergistic associations between these fungal guilds with plant richness and productivity operated in concert to promote positive richness-productivity relationships. Our findings provide empirical evidence for the importance of soil fungal guilds in integrating the linkages of plant richness and productivity, and suggest that future work incorporating soil fungal communities into richness-productivity relationships would advance our mechanistic understanding of their linkages.

Improved Protocol for DNA Extraction from Subsoils Using Phosphate Lysis Buffer

As our understanding of soil biology deepens, there is a growing demand for investigations addressing microbial processes in the earth beneath the topsoil layer, called subsoil. High clay content in subsoils often hinders the recovery of sufficient quantities of DNA as clay particles bind nucleic acids. Here, an efficient and reproducible DNA extraction method for 200 mg dried soil based on sodium dodecyl sulfate (SDS) lysis in the presence of phosphate buffer has been developed. The extraction protocol was optimized by quantifying bacterial 16S and fungal 18S rRNA genes amplified from extracts obtained by different combinations of lysis methods and phosphate buffer washes. The combination of one minute of bead beating, followed by ten min incubation at 65°C in the presence of 1 M phosphate buffer with 0.5% SDS, was found to produce the best results. The optimized protocol was compared with a commonly used cetyltrimethylammonium bromide (CTAB) method, using Phaeozem soil collected from 60 cm depth at a conventional agricultural field and validated on five subsoils. The reproducibility and robustness of the protocol was corroborated by an interlaboratory comparison. The DNA extraction protocol offers a reproducible and cost-effective tool for DNA-based studies of subsoil biology.

Observed variation in soil properties can drive large variation in modelled forest functioning and composition during tropical forest secondary succession

Censuses of tropical forest plots reveal large variation in biomass and plant composition. This paper evaluates whether such variation can emerge solely from realistic variation in a set of commonly measured soil chemical and physical properties. Controlled simulations were performed using a mechanistic model that includes forest dynamics, microbe-mediated biogeochemistry, and competition for nitrogen and phosphorus. Observations from 18 forest inventory plots in Guanacaste, Costa Rica were used to determine realistic variation in soil properties. In simulations of secondary succession, the across-plot range in plant biomass reached 30% of the mean and was attributable primarily to nutrient limitation and secondarily to soil texture differences that affected water availability. The contributions of different plant functional types to total biomass varied widely across plots and depended on soil nutrient status. In Central America, soil-induced variation in plant biomass increased with mean annual precipitation because of changes in nutrient limitation. In Central America, large variation in plant biomass and ecosystem composition arises mechanistically from realistic variation in soil properties. The degree of biomass and compositional variation is climate sensitive. In general, model predictions can be improved through better representation of soil nutrient processes, including their spatial variation.

Small-scale and multi-species approaches for assessing litter decomposition and soil dynamics in high-diversity forests

PREMISE OF THE STUDY

The relationship between tree species abundance and diversity and soil chemistry has been studied in several ecosystems and at different spatial scales. However, species-specific assessments have mainly been conducted in temperate ecosystems and in monospecific settings, calling for studies from diverse, mixed forests from different ecosystems.

METHODS

In a subtropical forest in southern China, under four dominant tree canopy species (Lithocarpus chintungensis, Castanopsis wattii, Schima noronhae, and Manglietia insignis), we assessed species' effect on inter- and intraspecific percentages of litter mass loss, and the effect of species on soil nutrients and soil microbial biomass.

RESULTS

Our results show significant differences in litter decomposition for all four species; however, the percentage of litter mass loss was stable under different species. Microbial biomass and soil nutrients presented strong differences under different tree species. Species-specific differences in soil characteristics were seen for carbon-nitrogen-phosphorus relationships. Surprisingly, the correlations between carbon and phosphorus and between nitrogen and phosphorus showed opposite slopes in soils collected under different tree species.

DISCUSSION

Our results provide insights into the importance of tree species identity in providing variety to ecosystem processes occurring on the forest floor. We recommend this methodological approach-combining analysis of litter decomposition, soil nutrient concentrations, and microbial biomass-when dealing with species-rich forests.

Nitrogen-fixing red alder trees tap rock-derived nutrients

Symbiotic nitrogen (N)-fixing trees supply significant N inputs to forest ecosystems, leading to increased soil fertility, forest growth, and carbon storage. Rapid growth and stoichiometric constraints of N fixers also create high demands for rock-derived nutrients such as phosphorus (P), while excess fixed N can generate acidity and accelerate leaching of rock-derived nutrients such as calcium (Ca). This ability of N-fixing trees to accelerate cycles of Ca, P, and other rock-derived nutrients has fostered speculation of a direct link between N fixation and mineral weathering in terrestrial ecosystems. However, field evidence that N-fixing trees have enhanced access to rock-derived nutrients is lacking. Here we use strontium (Sr) isotopes as a tracer of nutrient sources in a mixed-species temperate rainforest to show that N-fixing trees access more rock-derived nutrients than nonfixing trees. The N-fixing tree red alder (Alnus rubra), on average, took up 8 to 18% more rock-derived Sr than five co-occurring nonfixing tree species, including two with high requirements for rock-derived nutrients. The increased access to rock-derived nutrients occurred despite spatial variation in community-wide Sr sources across the forest, and only N fixers had foliar Sr isotopes that differed significantly from soil exchangeable pools. We calculate that increased uptake of rock-derived nutrients by N-fixing alder requires a 64% increase in weathering supply of nutrients over nonfixing trees. These findings provide direct evidence that an N-fixing tree species can also accelerate nutrient inputs from rock weathering, thus increasing supplies of multiple nutrients that limit carbon uptake and storage in forest ecosystems.

Reducing water use by alternate-furrow irrigation with livestock wastewater reduces antibiotic resistance gene abundance in the rhizosphere but not in the non-rhizosphere

Livestock wastewater is rich in nutrients but may contain antibiotics and antibiotic resistance genes (ARGs). Their discharge to watercourses or soil may result in proliferation of ARGs. Irrigation with wastewater appears to be the most feasible option of disposing of it. One efficient irrigation technology used in arid regions is alternate-furrow irrigation (AFI) by alternately drying part of the plant roots for a prolonged period to physiologically reduce transpiration without compromising yield. However, the extent to which AFI with wastewater influences the concentration of antibiotics and spread of ARGs in soil is poorly understood. The purpose of this paper is to investigate how AFI using swine wastewater alters antibiotic kinetics and ARGs abundance under different irrigation rates, using pepper as the model plant. We examined three AFI treatments using 50%, 65% and 80% of the amount of water employed in sufficient conventional furrow irrigation. Each treatment had a groundwater irrigation control. The results showed that antibiotic concentrations and relative ARGs abundance in the top 20 cm of soil did not increase with the irrigation amount, although they were higher than those in the groundwater-irrigated soils. The relative ARGs abundance in the soil was modulated by irrigation amount and reducing the irrigation amount in AFI reduced ARGs dispersion only in rhizosphere. When the soil moisture was close to field capacity, ARGs were more abundant in rhizosphere than in non-rhizosphere, possibly because the rhizosphere is rich in microbes and increasing antibiotic concentrations due to an increase in irrigation rate favors antibiotic-resistant microbiome in competing for substrates. These, however, were not mirrored in the relative ARGs abundance in the roots. These results have important implications as it revealed that reducing the input of antibiotics and ARGs into soil with AFI does not necessarily reduce ARGs proliferation.

Relationships Between Fungal and Plant Communities Differ Between Desert and Grassland in a Typical Dryland Region of Northwest China

The relationships between soil fungal and plant communities in the dryland have been well documented, yet the associated difference in relationships between soil fungal and plant communities among different habitats remains unclear. Here, we explored the relationships between plant and fungal functional communities, and the dominant factors of these fungal communities in the desert and grassland. Soil fungal functional communities were assessed based on fungal ITS sequence data which were obtained from our previous study. The results showed that the total, saprotrophic and pathotrophic fungal richness were predominantly determined by plant species richness and/or soil nutrients in the desert, but by MAP or soil CN in the grassland. AM fungal richness was only significantly related to soil nutrients in two habitats. The total and saprotrophic fungal species compositions were mainly shaped by abiotic and spatial factors in the desert, but by plant and abiotic factors in the grassland. Pathotrophic fungal species composition was more strongly correlated with plant and spatial factors in the desert, but with spatial and abiotic factors in the grassland. AM fungal species composition was more strongly correlated with MAP in the grassland, but with no factors in the desert. These results provide robust evidence that the relationships between soil fungal and plant communities, and the drivers of soil fungal communities differ between the desert and grassland. Furthermore, we highlight that the linkages between soil fungal and plant communities, and the drivers of soil fungal communities may also be affected by fungal traits (e.g., functional groups).

Fungal Communities Along a Small-Scale Elevational Gradient in an Alpine Tundra Are Determined by Soil Carbon Nitrogen Ratios

Elevational gradients are associated not only with variations in temperature and precipitation, but also with shifts in vegetation types and changes in soil physicochemical properties. While large-scale elevational patterns of soil microbial diversity, such as monotonic declines and hump-shaped models, have been reported, it is unclear whether within-ecosystem elevational distribution patterns exist for soil fungal communities at the small scale. Using Illumina Miseq DNA sequencing, we present a comprehensive analysis of soil fungal diversity and community compositions in an alpine tundra ecosystem at elevations ranging from 2000 to 2500 m on the Changbai Mountain, China. Soil fungal community composition differed among elevations, and the fungal diversity (i.e., species richness and Chao1) increased along elevations. Soil fungal richness was negatively correlated with soil carbon/nitrogen (C/N) ratio, and community composition varied according to the C/N ratio. In addition, the relative abundances of Basidiomycota and Leotiomycetes were similarly negatively correlated with C/N ratio. For functional guilds, our data showed that mycoparasite and foliar epiphyte abundances were also influenced by C/N ratio. These results indicated that soil C/N ratio might be a key factor in determining soil fungal distribution at small-scale elevational gradients.

Soil abiotic variables are more important than Salicaceae phylogeny or habitat specialization in determining soil microbial community structure

Predicting the outcome of interspecific interactions is a central goal in ecology. The diverse soil microbes that interact with plants are shaped by different aspects of plant identity, such as phylogenetic history and functional group. Species interactions may also be strongly shaped by abiotic environment, but there is mixed evidence on the relative importance of environment, plant identity and their interactions in shaping soil microbial communities. Using a multifactor, split-plot field experiment, we tested how hydrologic context, and three facets of Salicaceae plant identity-habitat specialization, phylogenetic distance and species identity-influence soil microbial community structure. Analysis of microbial community sequencing data with generalized dissimilarity models showed that abiotic environment explained up to 25% of variation in community composition of soil bacteria, fungi and archaea, while Salicaceae identity influenced <1% of the variation in community composition of soil microbial taxa. Multivariate linear models indicated that the influence of Salicaceae identity was small, but did contribute to differentiation of soil microbes within treatments. Moreover, results from a microbial niche breadth analysis show that soil microbes in wetlands have more specialized host associations than soil microbes in drier environments-showing that abiotic environment changed how plant identity correlated with soil microbial communities. This study demonstrates the predominance of major abiotic factors in shaping soil microbial community structure; the significance of abiotic context to biotic influence on soil microbes; and the utility of field experiments to disentangling the abiotic and biotic factors that are thought to be most essential for soil microbial communities.

Arbuscular mycorrhizal colonization has little consequence for plant heavy metal uptake in contaminated field soils

The factors affecting plant uptake of heavy metals from metalliferous soils are deeply important to the remediation of polluted areas. Arbuscular mycorrhizal fungi (AMF), soil-dwelling fungi that engage in an intimate exchange of nutrients with plant roots, are thought to be involved in plant metal uptake as well. Here, we used a novel field-based approach to investigate the effects of AMF on plant metal uptake from soils in Palmerton, Pennsylvania, USA contaminated with heavy metals from a nearby zinc smelter. Previous studies often focus on one or two plant species or metals, tend to use highly artificial growing conditions and metal applications, and rarely consider metals' effects on plants and AMF together. In contrast, we examined both direct and AMF-mediated effects of soil concentrations on plant concentrations of 8-13 metals in five wild plant species sampled across a field site with continuous variation in Zn, Pb, Cd, and Cu contamination. Plant and soil metal concentration profiles were closely matched despite high variability in soil metal concentrations even at small spatial scales. However, we observed few effects of soil metals on AMF colonization, and no effects of AMF colonization on plant metal uptake. Manipulating soil chemistry or plant community composition directly may control landscape-level plant metal uptake more effectively than altering AMF communities. Plant species identities may serve as highly local indicators of soil chemical characteristics.

Soil fungal diversity in natural grasslands of the Tibetan Plateau: associations with plant diversity and productivity

Previous studies have revealed inconsistent correlations between fungal diversity and plant diversity from local to global scales, and there is a lack of information about the diversity-diversity and productivity-diversity relationships for fungi in alpine regions. Here we investigated the internal relationships between soil fungal diversity, plant diversity and productivity across 60 grassland sites on the Tibetan Plateau, using Illumina sequencing of the internal transcribed spacer 2 (ITS2) region for fungal identification. Fungal alpha and beta diversities were best explained by plant alpha and beta diversities, respectively, when accounting for environmental drivers and geographic distance. The best ordinary least squares (OLS) multiple regression models, partial least squares regression (PLSR) and variation partitioning analysis (VPA) indicated that plant richness was positively correlated with fungal richness. However, no correlation between plant richness and fungal richness was evident for fungal functional guilds when analyzed individually. Plant productivity showed a weaker relationship to fungal diversity which was intercorrelated with other factors such as plant diversity, and was thus excluded as a main driver. Our study points to a predominant effect of plant diversity, along with other factors such as carbon : nitrogen (C : N) ratio, soil phosphorus and dissolved organic carbon, on soil fungal richness.

Tree species effects on pathogen-suppressive capacities of soil bacteria across two tropical dry forests in Costa Rica

Antibiotic-producing bacteria in the genus Streptomyces can inhibit soil-borne plant pathogens, and have the potential to mediate the impacts of disease on plant communities. Little is known about how antibiotic production varies among soil communities in tropical forests, despite a long history of interest in the role of soil-borne pathogens in these ecosystems. Our objective was to determine how tree species and soils influence variation in antibiotic-mediated pathogen suppression among Streptomyces communities in two tropical dry forest sites (Santa Rosa and Palo Verde). We targeted tree species that co-occur in both sites and used a culture-based functional assay to quantify pathogen-suppressive capacities of Streptomyces communities beneath 50 focal trees. We also measured host-associated litter and soil element concentrations as potential mechanisms by which trees may influence soil microbes. Pathogen-suppressive capacities of Streptomyces communities varied within and among tree species, and inhibitory phenotypes were significantly related to soil and litter element concentrations. Average proportions of inhibitory Streptomyces in soils from the same tree species varied between 1.6 and 3.3-fold between sites. Densities and proportions of pathogen-suppressive bacteria were always higher in Santa Rosa than Palo Verde. Our results suggest that spatial heterogeneity in the potential for antibiotic-mediated disease suppression is shaped by tree species, site, and soil characteristics, which could have significant implications for understanding plant community composition and diversity in tropical dry forests.

Biogeochemistry and Geographical Ecology: Embracing All Twenty-Five Elements Required to Build Organisms

Biogeochemistry is a key but relatively neglected part of the abiotic template that underlies ecology. The template has a geography, one that is increasingly being rearranged in this era of global change. Justus von Liebig's law of the minimum has played a useful role in focusing attention on biogeochemical regulation of populations, but given that ∼25+ elements are required to build organisms and that these organisms use and deplete nutrients in aggregates of communities and ecosystems, we make the case that it is time to move on. We review available models that suggest the many different mechanisms that give rise to multiple elements, or colimitation. We then review recent empirical data that show that rates of decomposition and primary productivity may be limited by multiple elements. In that light, given the tropics' high species diversity and generally more weathered soils, we predict that colimitation at community and ecosystem scales is more prevalent closer to the equator. We conclude with suggestions for how to move forward with experimental studies of colimitation.

Temporal and Spatial Variation of Soil Bacteria Richness, Composition, and Function in a Neotropical Rainforest

The high diversity of tree species has traditionally been considered an important controller of belowground processes in tropical rainforests. However, soil water availability and resources are also primary regulators of soil bacteria in many ecosystems. Separating the effects of these biotic and abiotic factors in the tropics is challenging because of their high spatial and temporal heterogeneity. To determine the drivers of tropical soil bacteria, we examined tree species effects using experimental tree monocultures and secondary forests at La Selva Biological Station in Costa Rica. A randomized block design captured spatial variation and we sampled at four dates across two years to assess temporal variation. We measured bacteria richness, phylogenetic diversity, community composition, biomass, and functional potential. All bacteria parameters varied significantly across dates. In addition, bacteria richness and phylogenetic diversity were affected by the interaction of vegetation type and date, whereas bacteria community composition was affected by the interaction of vegetation type and block. Shifts in bacteria community richness and composition were unrelated to shifts in enzyme function, suggesting physiological overlap among taxa. Based on the observed temporal and spatial heterogeneity, our understanding of tropical soil bacteria will benefit from additional work to determine the optimal temporal and spatial scales for sampling. Understanding spatial and temporal variation will facilitate prediction of how tropical soil microbes will respond to future environmental change.

Scale-dependent variation in nitrogen cycling and soil fungal communities along gradients of forest composition and age in regenerating tropical dry forests

Rates of ecosystem nitrogen (N) cycling may be mediated by the presence of ectomycorrhizal fungi, which compete directly with free-living microbes for N. In the regenerating tropical dry forests of Central America, the distribution of ectomycorrhizal trees is affected by succession and soil parent material, both of which may exert independent influence over soil N fluxes. In order to quantify these interacting controls, we used a scale-explicit sampling strategy to examine soil N cycling at scales ranging from the microsite to ecosystem level. We measured fungal community composition, total and inorganic N pools, gross proteolytic rate, net N mineralization and microbial extracellular enzyme activity at multiple locations within 18 permanent plots that span dramatic gradients of soil N concentration, stand age and forest composition. The ratio of inorganic to organic N cycling was correlated with variation in fungal community structure, consistent with a strong influence of ectomycorrhiza on ecosystem-scale N cycling. However, on average, > 61% of the variation in soil biogeochemistry occurred within plots, and the effects of forest composition were mediated by this local-scale heterogeneity in total soil N concentrations. These cross-scale interactions demonstrate the importance of a spatially explicit approach towards an understanding of controls on element cycling.