Exploration of environmental factors governing soil microbial community composition is long overdue and now possible with improved methods for characterizing microbial communities. Previously, we ...observed that rice soil microbial communities were distinctly different from tomato soil microbial communities, despite management and seasonal variations within soil type. Potential contributing factors included types and amounts of organic inputs, organic carbon content, and timing and amounts of water inputs. Of these, both soil water content and organic carbon availability were highly correlated with observed differences in composition. We examined how organic carbon amendment (compost, vetch, or no amendment) and water additions (from air dry to flooded) affect microbial community composition. Using canonical correspondence analysis of phospholipid fatty acid data, we determined flooded, carbon-amended (+C) microcosm samples were distinctly different from other +C samples and unamended (-C) samples. Although flooding without organic carbon addition influenced composition some, organic carbon addition was necessary to substantially alter community composition. Organic carbon availability had the same general effects on microbial communities regardless of whether it was compost or vetch in origin. In addition, flooded samples, regardless of organic carbon inputs, had significantly lower ratios of fungal to bacterial biomarkers, whereas under drier conditions and increased organic carbon availability the microbial communities had higher proportions of fungal biomass. When comparing field and microcosm soil, flooded +C microcosm samples were most similar to field-collected rice soil, whereas all other treatments were more similar to field-collected tomato soil. Overall, manipulating water and carbon content selected for microbial communities similar to those observed when the same factors were manipulated at the field scale.
Soil microbial communities control critical ecosystem processes such as decomposition, nutrient cycling, and soil organic matter formation. Continental scale patterns in the composition and ...functioning of microbial communities are related to climatic, biotic, and edaphic factors such as temperature and precipitation, plant community composition, and soil carbon, nitrogen, and pH. Although these relationships have been well explored individually, the examination of the factors that may act directly on microbial communities vs. those that may act indirectly through other ecosystem properties has not been well developed. To further such understanding, we utilized structural equation modeling (SEM) to evaluate a set of hypotheses about the direct and indirect effects of climatic, biotic, and edaphic variables on microbial communities across the continental United States. The primary goals of this work were to test our current understanding of the interactions among climate, soils, and plants in affecting microbial community composition, and to examine whether variation in the composition of the microbial community affects potential rates of soil enzymatic activities. A model of interacting factors created through SEM shows several expected patterns. Distal factors such as climate had indirect effects on microbial communities by influencing plant productivity, soil mineralogy, and soil pH, but factors related to soil organic matter chemistry had the most direct influence on community composition. We observed that both plant productivity and soil mineral composition were important indirect influences on community composition at the continental scale, both interacting to affect organic matter content and microbial biomass and ultimately community composition. Although soil hydrolytic enzymes were related to the moisture regime and soil carbon, oxidative enzymes were also affected by community composition, reflected in the abundance of soil fungi. These results highlight that soil microbial communities can be modeled within the context of multiple interacting ecosystem properties acting both directly and indirectly on their composition and function, and this provides a rich and informative context with which to examine communities. This work also highlights that variation in climate, microbial biomass, and microbial community composition can affect maximum rates of soil enzyme activities, potentially influencing rates of decomposition and nutrient mineralization in soils.
Many terrestrial ecosystems are nutrient limited. Koerselman and Meuleman (1996) proposed critical foliar N:P values that could predict wetland nutrient deficiencies (N:P < 14, N limitation; N:P > ...16, P limitation). Although critical N:P values have potential as ecological and diagnostic tools, species differences in N and P requirements must be tested. The objectives of our experiments were 1) to determine if two desert species share critical N:P values, and 2) to assess the N:P tool's applicability in a non-wetland system. We studied two common, co-occurring North American desert shrubs, Chrysothamnus nauseosus spp. consimilis and Sarcobatus vermiculatus. Based on leaf N and P concentrations, effective mycorrhizal status, and leaf N:P, we predicted Chrysothamnus would be N limited and Sarcobatus would be P limited. During the 2000 and 2001 growing seasons, juvenile shrubs received N, P, N+P, or control treatments. To assess interaction with water limitation, other shrubs were irrigated and fertilized in 2001 (N+IR, P+IR, N+P+IR, control IR). Contrary to the predicted N limitation in Chrysothamnus, stem growth was 1.7-fold greater in P+IR plants relative to IR controls, although without irrigation Chrysothamnus did not respond to P addition. Also, contrary to the predicted P limitation in Sarcobatus, stem growth was 2.7-fold and 1.5-fold greater in N and N+IR plants, respectively, relative to their controls. Leaf N was significantly higher in N-treated Sarcobatus, both with and without irrigation. Our study suggests species-specific critical N:P values and that the N:P tool does not effectively predict desert shrub nutrient limitations. Species adapted to low nutrient conditions may not respond to increased nutrient availability due to water and nutrient co-limitation, lack of plasticity, or lower tissue nutrient requirements.
Theoretical and empirical work has established a positive relationship between resource availability and habitat invasibility. For nonnative invasive annual grasses, similar to other invasive ...species, invader success has been tied most often to increased nitrogen (N) availability. These observations have led to the logical assumption that managing soils for low N availability will facilitate restoration of invasive plant-dominated systems. Although invasive annual grasses pose a serious threat to a number of perennial-dominated ecosystems worldwide, there has been no quantitative synthesis evaluating the degree to which soil N management may facilitate restoration efforts. We used meta-analysis to evaluate the degree to which soil N management impacts growth and competitive ability of annual and perennial grass seedlings. We then link our analysis to current theories of plant ecological strategies and community assembly to improve our ability to understand how soil N management may be used to restore annual grass-dominated communities. Across studies, annual grasses maintained higher growth rates and greater biomass and tiller production than perennials under low and high N availability. We found no evidence that lowering N availability fundamentally alters competitive interactions between annual and perennial grass seedlings. Competitive effects of annual neighbors on perennial targets were similar under low and high N availability. Moreover, in most cases perennials grown under competition in high-N soils produced more biomass than perennials grown under competition in low-N soils. While these findings counter current restoration and soil N management assumptions, these results are consistent with current plant ecological strategy and community assembly theory. Based on our results and these theories we argue that, in restoration scenarios in which the native plant community is being reassembled from seed, soil N management will have no direct positive effect on native plant establishment unless invasive plant propagule pools and priority effects are controlled the first growing season.
The composition of microbial communities responds to soil resource availability, and has been shown to vary with increasing depth in the soil profile. Soil microorganisms partly rely on root-derived ...carbon (C) for growth and activity. Roots in woody perennial systems like vineyards have a deeper vertical distribution than grasslands and annual agriculture. Thus, we hypothesized that vineyard soil microbial communities along a vertical soil profile would differ from those observed in grassland and annual agricultural systems. In a Pinot noir vineyard, soil pits were excavated to ca. 1.6–2.5m, and microbial community composition in ‘bulk’ (i.e., no roots) and ‘root’ (i.e., roots present) soil was described by phospholipid ester-linked fatty acids (PLFA). Utilization of soil taxonomy aided in understanding relationships between soil microbial communities, soil resources and other physical and chemical characteristics. Soil microbial communities in the Ap horizon were similar to each other, but greater variation in microbial communities was observed among the lower horizons. Soil resources (i.e., total PLFA, or labile C, soil C and nitrogen, and exchangeable potassium) were enriched in the surface horizons and significantly explained the distribution of soil microbial communities with depth. Soil chemical properties represented the secondary gradient explaining the differentiation between microbial communities in the B-horizons from the C-horizons. Relative abundance of Gram-positive bacteria and actinomycetes did not vary with depth, but were enriched in ‘root’ vs. ‘bulk’ soils. Fungal biomarkers increased with increasing depth in ‘root’ soils, differing from previous studies in grasslands and annual agricultural systems. This was dependent on the deep distribution of roots in the vineyard soil profile, suggesting that the distinct pattern in PLFA biomarkers may have been strongly affected by C derived from the grapevine roots. Gram-negative bacteria did not increase in concert with fungal abundance, suggesting that acidic pHs in lower soil horizons may have discouraged their growth. These results emphasize the importance of considering soil morphology and associated soil characteristics when investigating effects of depth and roots on soil microorganisms, and suggest that vineyard management practices and deep grapevine root distribution combine to cultivate a unique microbial community in these soil profiles.
Fungi and bacteria are the two dominant groups of soil microbial
communities worldwide. By controlling the turnover of soil organic matter,
these organisms directly regulate the cycling of carbon ...between the soil and
the atmosphere. Fundamental differences in the physiology and life history
of bacteria and fungi suggest that variation in the biogeography of relative abundance of soil fungi versus bacteria could drive striking differences in
carbon decomposition and soil organic matter formation between different
biomes. However, a lack of global and predictive information on the
distribution of these organisms in terrestrial ecosystems has prevented the
inclusion of relative abundance of soil fungi versus bacteria and the associated
processes in global biogeochemical models. Here, we used a global-scale
dataset of >3000 distinct observations of abundance of soil fungi versus bacteria in the surface topsoil (up to 15 cm) to generate the
first quantitative and high-spatial-resolution (1 km2) explicit map of
soil fungal proportion, defined as fungi/fungi + bacteria, across
terrestrial ecosystems. We reveal striking latitudinal trends where fungal
dominance increases in cold and high-latitude environments with large soil
carbon stocks. There was a strong nonlinear response of fungal dominance to the
environmental gradient, i.e., mean annual temperature (MAT) and net primary
productivity (NPP). Fungi dominated in regions with low MAT and NPP and bacteria dominated in regions with high MAT and NPP, thus representing slow vs. fast soil energy
channels, respectively, a concept with a long history in soil ecology. These
high-resolution models provide the first steps towards representing the
major soil microbial groups and their functional differences in global
biogeochemical models to improve predictions of soil organic matter turnover
under current and future climate scenarios. Raw datasets and global maps
generated in this study are available at https://doi.org/10.6084/m9.figshare.19556419 (Yu, 2022).
Nutrients, in addition to water, limit desert primary productivity, but nutrient limitations to fecundity and seed quality in desert ecosystems have received little attention. Reduced seed production ...and quality may affect recruitment, population, and community processes. At the Mono Basin, CA, USA where the alkaline, sandy soil has very low availability of N, P, and most other nutrients, seed production, recruitment, and dominance of the desert shrub Sarcobatus vermiculatus decrease over a dune successional sequence. Concurrently, Sarcobatus leaf N, P, and Ca/Mg ratio decline from early to later successional dunes. At two later successional dune sites, we fertilized adult Sarcobatus shrubs for 2 years and determined which nutrient(s) limited growth, seed production, and seed quality. We also tested whether nutrient addition at these older sites made these fitness-related variables equivalent to a younger, high-fecundity site. Nitrogen addition, alone, increased Sarcobatus leaf N, growth, and seed production per shoot module. Any treatment including P, Ca, Mg, or micronutrients but not N had an insignificant effect on growth and fecundity. Nitrogen addition also increased filled seed weight, a predictor of potential seedling survival, at one of the sites. Nitrogen-limited seed production and seed mass may reduce Sarcobatus fitness and contribute to the observed successional changes in plant community composition in this alkaline desert ecosystem.
Both water and nutrients are limiting in arid environments, and desert plants have adapted to these limitations through numerous developmental and physiological mechanisms. In the Mono Basin, ...California, USA, co-dominant Sarcobatus vermiculatus and Chrysothamnus nauseosus ssp. consimilis are differentially N and P limited. We hypothesized that low leaf N resorption contributes to N-limitation in Sarcobatus and that low leaf P resorption contributes to P-limitation in Chrysothamnus. As predicted, Sarcobatus resorbed proportionally 1.7-fold less N than Chrysothamnus, but reduced leaf P in senescent leaves to lower levels than Chrysothamnus (8.0-10.8-fold lower based on leaf area or mass, respectively), consistent with N, but not P limitations in Sarcobatus. Again, as predicted, Chrysothamnus resorbed proportionally 2.0-fold less P than Sarcobatus yet reduced leaf N in senescent leaves to lower levels than Sarcobatus (1.8-1.3-fold lower based on leaf area or mass, respectively), consistent with P, but not N limitations in Chrysothamnus. Leaf N and P pools were approximately 50% of aboveground pools in both species during the growing season, suggesting leaf resorption can contribute significantly to whole plant nutrient retention. This was consistent with changes in leaf N vs. P concentration as plants grew from seedlings to adults. Our results support the conclusion that N-limitation in Sarcobatus and P-limitation in Chrysothamnus are in part caused by physiological (or other) constraints that prevent more efficient resorption of N or P, respectively. For these species, differential nutrient resorption may be a key physiological component contributing to their coexistence in this saline, low resource habitat.
Phospholipid fatty acid (PLFA) and total soil fatty acid methyl esters (TSFAME), both lipid-based approaches used to characterize microbial communities, were compared with respect to their reliable ...detection limits, extraction precision, and ability to differentiate agricultural soils. Two sets of soil samples, representing seven crop types from California's Central Valley, were extracted using PLFA and TSFAME procedures. PLFA analysis required 10 times more soil than TSFAME analysis to obtain a reliable microbial community fingerprint and total fatty acid content measurement. Although less soil initially was extracted with TSFAME, total fatty acid (FA) content g−1 soil (DW) was more than 7-fold higher in TSFAME– versus PLFA-extracted samples. Sample extraction precision was much lower with TSFAME analysis than PLFA analysis, with the coefficient of variation between replicates being as much as 4-fold higher with TSFAME extraction. There were significant differences between PLFA– and TSFAME-extracted samples when biomarker pool sizes (mol% values) for bacteria, actinomycetes, and fungi were compared. Correspondence analysis (CA) of PLFA and TSFAME samples indicated that extraction method had the greatest influence on sample FA composition. Soil type also influenced FA composition, with samples grouping by soil type with both extraction methods. However, separate CAs of PLFA– and TSFAME extracted samples depicted strong differences in underlying sample groupings. Recommendations for the selection of extraction method are presented and discussed.
Invasion by exotic annual grasses is one of the most significant threats to arid ecosystems in the western USA. Current theories of invasibility predict plant communities become more susceptible to ...invasion whenever there is an increase in the amount of unused resources. The objective of this field study was to examine how resource pulses and temporal variation in resource demand by the native shrub vegetation influences establishment of the invasive annual grass
Schismus arabicus. Water and nitrogen were applied as pulses in early spring, mid-spring, or continuously throughout the growing season to plots containing either
Atriplex confertifolia or
Atriplex parryi shrubs. The effect of resource pulses on
Schismus density and biomass was highly dependent on the seasonal timing of the resource pulses and the identity of the neighbor shrub. When resource pulses coincided with high rates of resource capture and growth of the native vegetation, density and biomass of
Schismus was reduced.
Schismus establishment was greater under continuous resource supply compared to pulsed resource supply, likely because more soil resources were available at a shallow depth when resources were supplied at a continuous low rate. These results suggest that the establishment of invasive annual grasses in arid systems can be influenced by the magnitude and spatial distribution of resource pulses in addition to the seasonal timing of resource pulses.
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