Use of the signature Fatty Acid 16:1ω5 as a tool to determine the distribution of arbuscular mycorrhizal fungi in soil

Invasion alters plant and mycorrhizal communities in an alpine tussock grassland

Plant invasions are impacting alpine zones, altering key mutualisms that affect ecosystem functions. Plant-mycorrhizal associations are sensitive to invasion, but previous studies have been limited in the types of mycorrhizas examined. Consequently, little is known about how invaders that host rarer types of mycorrhizas may affect community and ecosystem properties. We studied invasion by an ericoid mycorrhizal host plant (Calluna vulgaris L., heather) in alpine tussock grasslands in New Zealand. We investigate the effects of increasing C. vulgaris density on the plant and soil microbial community and on mycorrhization in the dominant native species (Chionochloa rubra Z., red tussock), an arbuscular mycorrhizal host. We show that variation in plant community composition was primarily driven by invader density. High invader densities were associated with reductions in C. rubra diameter and in the cover, richness and diversity of the subordinate plant community. Belowground, we show that higher invader densities were associated with lower rates of mycorrhization in C. rubra and higher proportional abundance of the fungal lipid biomarker 18:2ω6 but had little effect on total microbial biomass, which may suggest increased ericoid mycorrhizal and fine root biomass in high C. vulgaris density stands. Our data suggest that disruption of native plant-arbuscular mycorrhizal networks may contribute to the competitive success of C. vulgaris, and that the dramatic decline of C. rubra with invasion reflects its relatively high mycorrhizal dependence. By exploring invasion of a plant with a less common mycorrhizal type, our study expands knowledge of the ecosystem consequences of biological invasions.

Efficiently recording and processing data from arbuscular mycorrhizal colonization assays using AMScorer and AMReader

Arbuscular mycorrhizal (AM) fungi engage with land plants in a widespread, mutualistic endosymbiosis which provides their hosts with increased access to nutrients and enhanced biotic and abiotic stress resistance. The potential for reducing fertiliser use and improving crop resilience has resulted in rapidly increasing scientific interest. Microscopic quantification of the level of AM colonization is of fundamental importance to this research, however the methods for recording and processing these data are time-consuming and tedious. In order to streamline these processes, we have developed AMScorer, an easy-to-use Excel spreadsheet, which enables the user to record data rapidly during from microscopy-based assays, and instantly performs the subsequent data processing steps. In our hands, AMScorer has more than halved the time required for data collection compared to paper-based methods. Subsequently, we developed AMReader, a user-friendly R package, which enables easy visualization and statistical analyses of data from AMScorer. These tools require only limited skills in Excel and R, and can accelerate research into AM symbioses, help researchers with variable resources to conduct research, and facilitate the storage and sharing of data from AM colonization assays. They are available for download at https://github.com/EJarrattBarnham/AMReader, along with an extensive user manual.

Mass Production of Arbuscular Mycorrhizal Fungi on the Sorghum Plants Inoculated with Burkholderia arboris Using Soybean Mill Waste and Vermicompost-Amended Soil-Sand Substrate

Arbuscular mycorrhizal (AM) fungi are being used as a new generation of biofertilizers to increase plant growth by improving plant nutrition and bio-protection. However, because of the obligatory nature of the plant host, large-scale multiplication of AM propagules is challenging, which limits its applicability. This study evaluates the ability of Burkholderia arboris to increase AM production in soybean mill waste and vermicompost amended by soil-sand mixture planted with sorghum as a host plant. The experiment was conducted in a nursery using a completely randomized design with four inoculation treatments (B. arboris, AM fungi, B. arboris + AM fungi, and control) under sterilized and unsterilized conditions. AM production was investigated microscopically (spore density and root colonization), and biochemically (AM-specific lipid biomarker, 16:1ω5cis derived from neutral lipid fatty acid (NLFA), and phospholipid fatty acid (PLFA) fractions from both soil and roots). Integrating B. arboris with AM fungi in organically amended pots was found to increase AM fungal production by 62.16 spores g-1 soil and root colonization by 80.85%. Biochemical parameters also increased with B. arboris inoculation: 5.49 nmol PLFA g-1 soil and 692.68 nmol PLFA g-1 root and 36.72 nmol NLFA g-1 soil and 3147.57 nmol NLFA g-1 root. Co-inoculation also increased glomalin-related soil protein and root biomass. Principal component analysis (PCA) further supported the higher contribution of B. arboris to AM fungi production under unsterilized conditions. In conclusion, inoculation of AM plant host seeds with B. arboris prior to sowing into organic potting mix could be a promising and cost-effective approach for increasing AM inoculum density for commercial production. Furthermore, efforts need to be made for up-scaling the AM production with different plant hosts and soil-substrate types.

Negative effects of phosphorus addition outweigh effects of arbuscular mycorrhizal fungi and nitrogen addition on grassland temporal stability in the eastern Eurasian desert steppe

The temporal stability of grassland plant communities is substantially affected by soil nutrient enrichment. However, the potential main and interactive effects of arbuscular mycorrhizal fungi (AMF) and soil nitrogen (N) and phosphorus (P) enrichment on the stability of plant productivity have not yet been clarified. We combined a three-year in situ field experiment to assess the impacts of soil fertilization and AMF on the stability of plant productivity. P addition decreased the stability of plant productivity by increasing the standard deviation relative to the mean of plant productivity. However, compared to species richness, the stability of C3 grasses and other functional groups asynchrony were the most important drivers changing the stability of plant productivity. The negative impacts of P addition overrode the impacts of AMF on the stability of plant productivity. Overall, our study suggests the importance of soil nutrient availability over AMF in terms of shaping the stability of plant productivity. Our results also suggest that three-year anthropogenic soil nutrient enrichment could reduce the stability of plant communities in grassland regardless of AMF in the P-limited grassland ecosystem.

Functions of Lipids in Development and Reproduction of Arbuscular Mycorrhizal Fungi

Arbuscular mycorrhizal fungi (AMF) form mutualistic associations with most land plants. The symbiosis is based on the exchange of nutrients: AMF receive photosynthetically fixed carbon from the plants and deliver mineral nutrients in return. Lipids are important players in the symbiosis. They act as components of the plant-derived membrane surrounding arbuscules, as carbon sources transferred from plants to AMF, as a major form of carbon storage in AMF and as triggers of developmental responses in AMF. In this review, we describe the role of lipids in arbuscular mycorrhizal symbiosis and AMF development.

Application of dry olive residue-based biochar in combination with arbuscular mycorrhizal fungi enhances the microbial status of metal contaminated soils

Biochar made-up of dry olive residue (DOR), a biomass resulting from the olive oil extraction industry, has been proposed to be used as a reclamation agent for the recovery of metal contaminated soils. The aim of the present study was to investigate whether the soil application of DOR-based biochar alone or in combination with arbuscular mycorrhizal fungi (AMF) leads to an enhancement in the functionality and abundance of microbial communities inhabiting metal contaminated soils. To study that, a greenhouse microcosm experiment was carried out, where the effect of the factors (i) soil application of DOR-based biochar, (ii) biochar pyrolysis temperature (considering the variants 350 and 500 °C), (iii) soil application dose of biochar (2 and 5%), (iv) soil contamination level (slightly, moderately and highly polluted), (v) soil treatment time (30, 60 and 90 days) and (vi) soil inoculation with Funneliformis mosseae (AM fungus) on β-glucosidase and dehydrogenase activities, FA (fatty acid)-based abundance of soil microbial communities, soil glomalin content and AMF root colonization rates of the wheat plants growing in each microcosm were evaluated. Biochar soil amendment did not stimulate enzyme activities but increased microbial abundances. Dehydrogenase activity and microbial abundances were found to be higher in less contaminated soils and at shorter treatment times. Biochar pyrolysis temperature and application dose differently affected enzyme activities, but while the first factor did not have a significant effect on glucosidase and dehydrogenase, a higher biochar dose resulted in boosted microbial abundances. Soil inoculation with F. mosseae favored the proliferation of soil AMF community and increased soil glomalin content as well as rates of AMF root colonization. This factor also interacted with many of the others evaluated to significantly affect soil enzyme activities, microbial abundances and AMF community. Our results indicate that the application of DOR-based biochar along with AMF fungi is an appropriate approach to improve the status of microbial communities in soils with a moderate metal contamination at short-term.

Microbial community development in tropical constructed wetland soils in Taiwan

Constructed wetlands are widely used around the world as a low-cost wastewater treatment system that simultaneously provides various ecosystem services. Microorganisms in wetland soils serve as fundamental producers and decomposers that support wetland functions. However, few studies have documented the compositions of soil microorganisms in constructed wetland systems and even fewer have evaluated how soil microorganisms change after a wetland is constructed. In this study, soil samples were collected from four constructed wetlands of different ages and analyzed with a phospholipid fatty acid (PLFA) method to show how soil microbial communities change overtime. The results were that both the bacterial and fungal abundances increased with wetland age, and bacteria comprised about 90% of the soil microbial communities in all ages of constructed wetlands. Although the compositions of microbial communities remained similar among the wetlands, the stress indices showed that microbial stress may be affected by changes in the availability of in situ nutrients, e.g. ammonium, nitrate_, soluble organic nitrogen and total dissolved nitrogen.

Ecological memory of recurrent drought modifies soil processes via changes in soil microbial community

Climate change is altering the frequency and severity of drought events. Recent evidence indicates that drought may produce legacy effects on soil microbial communities. However, it is unclear whether precedent drought events lead to ecological memory formation, i.e., the capacity of past events to influence current ecosystem response trajectories. Here, we utilize a long-term field experiment in a mountain grassland in central Austria with an experimental layout comparing 10 years of recurrent drought events to a single drought event and ambient conditions. We show that recurrent droughts increase the dissimilarity of microbial communities compared to control and single drought events, and enhance soil multifunctionality during drought (calculated via measurements of potential enzymatic activities, soil nutrients, microbial biomass stoichiometry and belowground net primary productivity). Our results indicate that soil microbial community composition changes in concert with its functioning, with consequences for soil processes. The formation of ecological memory in soil under recurrent drought may enhance the resilience of ecosystem functioning against future drought events.

Legacies of past ecological disturbances are expected but challenging to demonstrate. Here the authors report a 10-year field experiment in a mountain grassland that shows ecological memory of soil microbial community and functioning in response to recurrent drought.

Multidimensional trophic niche revealed by complementary approaches: Gut content, digestive enzymes, fatty acids and stable isotopes in Collembola

Trophic niche differentiation may explain coexistence and shape functional roles of species. In complex natural food webs, however, trophic niche parameters depicted by single and isolated methods may simplify the multidimensional nature of consumer trophic niches, which includes feeding processes such as food choice, ingestion, digestion, assimilation and retention. Here we explore the correlation and complementarity of trophic niche parameters tackled by four complementary methodological approaches, that is, visual gut content, digestive enzyme, fatty acid and stable isotope analyses-each assessing one or few feeding processes, and demonstrate the power of method combination. Focusing on soil ecosystems, where many omnivore species with cryptic feeding habits coexist, we chose Collembola as an example. We compiled 15 key trophic niche parameters for 125 species from 40 studies. We assessed correlations among trophic niche parameters and described variation of these parameters in different Collembola species, families and across life-forms, which represent microhabitat specialisation. Correlation between trophic niche parameters was weak in 45 out of 64 pairwise comparisons, pointing at complementarity of the four methods. Jointly, the results indicated that fungal- and plant-feeding Collembola assimilate storage, rather than structural polysaccharides, and suggested bacterial feeding as a potential alternative feeding strategy. Gut content and fatty acid analyses suggested alignment between ingestion and assimilation/retention processes in fungal- and plant-feeding Collembola. From the 15 trophic niche parameters, six were related to Collembola family identity, suggesting that not all trophic niche dimensions are phylogenetically structured. Only three parameters were related to the life-forms, suggesting that species use various feeding strategies when living in the same microenvironments. Consumers can meet their nutritional needs by varying their food choices, ingestion and digestion strategies, with the connection among different feeding processes being dependent on the consumed resource and consumer adaptations. Multiple methods reveal different dimensions, together drawing a comprehensive picture of the trophic niche. Future studies applying the multidimensional trophic niche approach will allow us to trace trophic complexity and reveal niche partitioning of omnivorous species and their functional roles, especially in cryptic environments such as soils, caves, deep ocean or benthic ecosystems.

Soybean Processing Mill Waste Plus Vermicompost Enhances Arbuscular Mycorrhizal Fungus Inoculum Production

This study considered soybean processing mill waste (hulls) as an organic substrate for mass multiplication of indigenous arbuscular mycorrhizal (AM) fungi on sorghum and amaranthus as hosts. In the first experiment, from seven soybean processing mill wastes, three wastes were evaluated for their ability to multiply AM fungi on the two host plants. Among these wastes, hulls were found to be promising for the multiplication of AM fungi and were further examined in a second experiment in combination with vermicompost (VC), a mix of hulls plus vermicompost (SH + VC) amended with soil: sand mix (3:1 v/v) and a soil-sand mix used as a control (SS) in polybags containing the previous two host species. We found that SH blended with VC significantly improved AM fungus production in sorghum polybags assessed through microscopic (spore density in soil, colonization in roots) and biochemical parameters (AM signature lipids in soil: 16:1ω5cis neutral lipid fatty acid (NLFA); phospholipids fatty acid (PLFA) g-1 soil; 16:1ω5cis ester lipid fatty acid (ELFA) g-1 both in soil and roots; and glomalin content in soil. SH + VC contained significantly greater AM fungus populations than the other substrate combinations examined. Principal component analysis (PCA) also identified sorghum as a potential host supporting AM fungus populations particularly when grown under SH + VC conditions. Hence, the combination of soybean hulls and vermicompost was found to be a promising substrate for the mass production of AM fungi using sorghum as a host. These findings have important implications for developing AM fungus inoculum production strategies at the commercial scale.

Stable C and N isotope natural abundances of intraradical hyphae of arbuscular mycorrhizal fungi

Data for stable C and N isotope natural abundances of arbuscular mycorrhizal (AM) fungi are currently sparse, as fungal material is difficult to access for analysis. So far, isotope analyses have been limited to lipid compounds associated with fungal membranes or storage structures (biomarkers), fungal spores and soil hyphae. However, it remains unclear whether any of these components are an ideal substitute for intraradical AM hyphae as the functional nutrient trading organ. Thus, we isolated intraradical hyphae of the AM fungus Rhizophagus irregularis from roots of the grass Festuca ovina and the legume Medicago sativa via an enzymatic and a mechanical approach. In addition, extraradical hyphae were isolated from a sand-soil mix associated with each plant. All three approaches revealed comparable isotope signatures of R. irregularis hyphae. The hyphae were 13C- and 15N-enriched relative to leaves and roots irrespective of the plant partner, while they were enriched only in 15N compared with soil. The 13C enrichment of AM hyphae implies a plant carbohydrate source, whereby the enrichment was likely reduced by an additional plant lipid source. The 15N enrichment indicates the potential of AM fungi to gain nitrogen from an organic source. Our isotope signatures of the investigated AM fungus support recent findings for mycoheterotrophic plants which are suggested to mirror the associated AM fungi isotope composition. Stable isotope natural abundances of intraradical AM hyphae as the functional trading organ for bi-directional carbon-for-mineral nutrient exchanges complement data on spores and membrane biomarkers.

Community Structure of Arbuscular Mycorrhizal Fungi in Soils of Switchgrass Harvested for Bioenergy

Learning more about the biodiversity and composition of arbuscular mycorrhizal fungi (AMF) under alternative agricultural management scenarios may be important to the sustainable intensification of switchgrass grown as a bioenergy crop. Using PacBio single-molecule sequencing and taxonomic resolution to the level of amplicon sequence variant (ASV), we assessed the effects of nitrogen amendment on AMF associating with switchgrass and explored relationships between AMF and switchgrass yield across three sites of various productivities in Wisconsin. Nitrogen amendment had little effect on AMF diversity metrics or community composition. While AMF ASV diversity was not correlated with switchgrass yield, AMF family richness and switchgrass yield had a strong, positive relationship at one of our three sites. Each of our sites was dominated by unique ASVs of the species Paraglomus brasilianum, indicating regional segregation of AMF at the intraspecific level. Our molecular biodiversity survey identified putative core members of the switchgrass microbiome, as well as novel clades of AMF, especially in the order Paraglomerales and the genus Nanoglomus Furthermore, our phylogenies unite the cosmopolitan, soil-inhabiting clade deemed GS24 with Pervetustaceae, an enigmatic family prevalent in stressful environments. Future studies should isolate and characterize the novel genetic diversity found in switchgrass agroecosystems and explore the potential yield benefits of AMF richness.IMPORTANCE We assessed the different species of beneficial fungi living in agricultural fields of switchgrass, a large grass grown for biofuels, using high-resolution DNA sequencing. Contrary to our expectations, the fungi were not greatly affected by fertilization. However, we found a positive relationship between plant productivity and the number of families of beneficial fungi at one site. Furthermore, we sequenced many species that could not be identified with existing reference databases. One group of fungi was highlighted in an earlier study for being widely distributed but of unknown taxonomy. We discovered that this group belonged to a family called Pervetustaceae, which may benefit switchgrass in stressful environments. To produce higher-yielding switchgrass in a more sustainable manner, it could help to study these undescribed fungi and the ways in which they may contribute to greater switchgrass yield in the absence of fertilization.

Transition in the isotopic signatures of fatty-acid soil biomarkers under changing land use: Insights from a multi-decadal chronosequence

The effects of climate warming on soil erosion in upland ecosystems will be disproportionately higher than for lowlands due to steeper topography and higher predicted rainfall. Soil erosion may be enhanced by climate warming and upslope shifts in agriculture as conditions for plant growth improve. Identification of eroded-soil sources will inform land management practices that mitigate soil loss and impacts on aquatic receiving environments. Isotopic signatures of plant-derived fatty acid (FA) soil biomarkers can discriminate sediment sources and will detect shifts in land use and natural vegetation toposequences. Accounting for these isotopic shifts requires knowledge of the magnitude and time scale for transition in biomarker signatures. We examined a 30-year chronosequence to quantify the transition in isotopic values of bulk nitrogen, carbon and FA biomarkers following a change from pine forestry to pastoral agriculture in the central North Island of New Zealand. We found the transition in soil biomarker isotopic values was complete within 6 years, with substantial increases in both organic carbon (1% yr^-1) and total N (0.13% yr^-1) of top soils. Subsequent changes were negligible (i.e., <0.04% yr^-1), indicative of a new steady state. Similar patterns were observed in the isotopic signatures of bulk δ¹³C and δ¹⁵N values and FA δ¹³C values (i.e., ±0.5-0.6‰ yr^-1). Bulk C and N properties and the FAs C14:0, C16:0, C18:2, C24:0 and C26:0 displayed clear transitions from harvested pine to mature pasture. We found evidence that mycorrhizal fungi could disperse and influence soil FA isotopic signatures. This highlights the need to consider both harvested and mature forests in source-tracing studies. Finally, our study shows that near-instantaneous changes in land use associated with agriculture can alter the isotopic signatures of plant biomarkers in soils. This produces a step change that can be readily detected in sedimentary records.

Shifting systems: prerequisites for the application of quantitative fatty acid signature analysis in soil food webs

Quantitative fatty acid signature analysis (QFASA) is widely used to investigate trophic interactions in marine ecosystems, as nutritionally important ω3 long-chain polyunsaturated fatty acids at the food web base allow tracing of their trophic transfer in the food chain. By contrast, the basal resources in soil food webs comprise a wider array of trophic markers, including branched-chain, cyclopropane as well as several mono- and polyunsaturated fatty acids. These diverse markers allow distinguishing between the three dominant soil carbon and energy channels, the root, bacterial and fungal pathway. QFASA has not been applied yet to soil ecosystems owing to the lack of a priori data to fit the model. The present work investigates the transfer of absolute and relative trophic marker fatty acids into Collembola as dominant representatives of the soil mesofauna. Three different species were fed on a variety of single diets characteristic for the green and brown food chain. Calibration coefficients were calculated and diet estimation trials for mixed diet set-ups were performed, using a library comprising 50 different resources. However, estimation of Collembola diet was only partially successful, identifying the main components, but not the correct relative proportions. Adjustments by fat content or diet group exclusion did not improve the results. Nonetheless, this work provides, to our knowledge, a first comprehensive dataset to translate the application of QFASA from marine to soil ecosystems. This article is part of the theme issue 'The next horizons for lipids as 'trophic biomarkers': evidence and significance of consumer modification of dietary fatty acids'.

Non-symbiotic soil microbes are more strongly influenced by altered tree biodiversity than arbuscular mycorrhizal fungi during initial forest establishment

While the relationship between plant and microbial diversity has been well studied in grasslands, less is known about similar relationships in forests, especially for obligately symbiotic arbuscular mycorrhizal (AM) fungi. To assess the effect of varying tree diversity on microbial alpha- and beta-diversity, we sampled soil from plots in a high-density tree diversity experiment in Minnesota, USA, 3 years after establishment. About 3 of 12 tree species are AM hosts; the other 9 primarily associate with ectomycorrhizal fungi. We used phospho- and neutral lipid fatty acid analysis to characterize the biomass and functional identity of the whole soil bacterial and fungal community and high throughput sequencing to identify the species-level richness and composition of the AM fungal community. We found that plots of differing tree composition had different bacterial and fungal communities; plots with conifers, and especially Juniperus virginiana, had lower densities of several bacterial groups. In contrast, plots with a higher density or diversity of AM hosts showed no sign of greater AM fungal abundance or diversity. Our results indicate that early responses to plant diversity vary considerably across microbial groups, with AM fungal communities potentially requiring longer timescales to respond to changes in host tree diversity.

Diversity and specificity of lipid patterns in basal soil food web resources

Soil food webs are important drivers for key ecological functions in terrestrial systems such as carbon and nutrient cycling. However, soil food web models generally lack quantitative data, mainly due to the shortage in high-throughput methods to describe energy flows. In marine environments, multivariate optimization models (Quantitative Fatty Acid Signature Analysis) and Bayesian approaches (source-tracking algorithm) were established to predict the proportion of predator diets using lipids as tracers. A premise for the application of such models to soil systems is to acquire the fatty acid pattern of a broad range of resources and to reveal potential overlap in their signatures. We present a comprehensive comparison of lipid pattern across widespread taxa of plants (leaves and roots, n = 48), algae (n = 59), fungi (n = 60), and bacteria (n = 62) as basal food web resources. Lipid profiles from microorganisms and algae were assessed from laboratory cultures, whereas plant tissue was derived from an arable field. A lipid library was constructed and multivariate data analyses (hierarchical clustering, nMDS) was used to assess the extent of separation in lipid pattern by species or resource type. The performance of the lipid library was tested by leave-one-prey-out (LOPO) analysis, giving the distinctiveness of the resource (prey) groups. Fungi and plant leaves were correctly assigned based on their lipid pattern with more than 98%, while plant roots and bacteria achieved 88 and 85%, respectively. However, algae were only correctly classified by 60%, pointing to a bias in the herbivore food chain. Fatty acids most important for separation of algae and plant leaves were of the omega 3 type, i.e. 16:3ω3 and 18:3ω3. In plant roots 18:1ω9 was most important, whereas bacteria were distinguished predominantly by methyl-branched fatty acids. Overall, the lipid pattern of major soil food web resources are sufficiently differentiated to allow for qualitative (biomarker) analyses as well as quantitative modelling, yet with precaution in the case of algae.

Soil microbial restoration strategies for promoting climate-ready prairie ecosystems

Tractable practices for soil microbial restoration in tallgrass prairies reclaimed from agriculture are a critical gap in traditional ecological restoration. Long-term fertilization and tilling permanently alter soil bacterial and fungal communities, requiring microbe-targeted restoration methods to improve belowground ecosystem services and carbon storage in newly restored prairies. These techniques are particularly important when restoring for climate-ready ecosystems, adapted to altered temperature regimes. To approach these issues, we conducted a multi-factorial greenhouse experiment to test the effects of plant species richness, soil amendment and elevated temperature on soil microbial diversity, growth, and function. Treatments consisted of three seedlings of one plant species (Andropogon gerardii) or one seedling each of three plant species (A. gerardii, Echinacea pallida, Coreopsis lanceolata). Soil amendments included cellulose addition, inoculation with a microbial community collected from an undisturbed remnant prairie, and a control. We assessed microbial communities using extracellular enzyme assays, Illumina sequencing of the bacterial 16S rRNA gene, predicted bacterial metabolic pathways from sequence data and phospholipid fatty acid analysis (PLFA), which includes both bacterial and fungal lipid abundances. Our results indicate that addition of cellulose selects for slow-growing bacterial taxa (Verrucomicrobia) and fungi at ambient temperature. However, at elevated temperature, selection for slow-growing bacterial taxa is enhanced, while selection for fungi is lost, indicating temperature sensitivity among fungi. Cellulose addition was a more effective means of altering soil community composition than addition of microbial communities harvested from a remnant prairie. Soil water content was typically higher in the A. gerardii treatment alone, regardless of temperature, but at ambient temperature only, predicted metagenomics pathways for bacterial carbon metabolism were more abundant with A. gerardii. In summary, these results from a mesocosm test case indicate that adding cellulose to newly restored soil and increasing the abundance of C₄ grasses, such as A. gerardii, can select for microbial communities adapted for slow growth and carbon storage. Further testing is required to determine if these approaches yield the same results in a field-level experiment.

Drought-Induced Accumulation of Root Exudates Supports Post-drought Recovery of Microbes in Mountain Grassland

Droughts strongly affect carbon and nitrogen cycling in grasslands, with consequences for ecosystem productivity. Therefore, we investigated how experimental grassland communities interact with groups of soil microorganisms. In particular, we explored the mechanisms of the drought-induced decoupling of plant photosynthesis and microbial carbon cycling and its recovery after rewetting. Our aim was to better understand how root exudation during drought is linked to pulses of soil microbial activity and changes in plant nitrogen uptake after rewetting. We set up a mesocosm experiment on a meadow site and used shelters to simulate drought. We performed two ¹³C-CO₂ pulse labelings, the first at peak drought and the second in the recovery phase, and traced the flow of assimilates into the carbohydrates of plants and the water extractable organic carbon and microorganisms from the soil. Total microbial tracer uptake in the main metabolism was estimated by chloroform fumigation extraction, whereas the lipid biomarkers were used to assess differences between the microbial groups. Drought led to a reduction of aboveground versus belowground plant growth and to an increase of ¹³C tracer contents in the carbohydrates, particularly in the roots. Newly assimilated ¹³C tracer unexpectedly accumulated in the water-extractable soil organic carbon, indicating that root exudation continued during the drought. In contrast, drought strongly reduced the amount of ¹³C tracer assimilated into the soil microorganisms. This reduction was more severe in the growth-related lipid biomarkers than in the metabolic compounds, suggesting a slowdown of microbial processes at peak drought. Shortly after rewetting, the tracer accumulation in the belowground plant carbohydrates and in the water-extractable soil organic carbon disappeared. Interestingly, this disappearance was paralleled by a quick recovery of the carbon uptake into metabolic and growth-related compounds from the rhizospheric microorganisms, which was probably related to the higher nitrogen supply to the plant shoots. We conclude that the decoupling of plant photosynthesis and soil microbial carbon cycling during drought is due to reduced carbon uptake and metabolic turnover of rhizospheric soil microorganisms. Moreover, our study suggests that the maintenance of root exudation during drought is connected to a fast reinitiation of soil microbial activity after rewetting, supporting plant recovery through increased nitrogen availability.

Micro-decomposer communities and decomposition processes in tropical lowlands as affected by land use and litter type

We investigated how the land-use change from rainforest into jungle rubber, intensive rubber and oil palm plantations affects decomposers and litter decomposition in Sumatra, Indonesia. Litterbags containing three litter types were placed into four land-use systems and harvested after 6 and 12 months. Litter mass loss and litter element concentrations were measured, and different microbial groups including bacteria, fungi and testate amoebae were studied. After 12 months 81, 65, 63 and 53% of litter exposed in rainforest, jungle rubber in oil palm and rubber plantations was decomposed. In addition to land use, litter decomposition varied strongly with litter type and short-term effects differed markedly from long-term effects. After 6 months, oil palm and rubber litter decomposed faster than rainforest litter, but after 12 months, decomposition of rainforest litter exceeded that of oil palm and rubber litter, reflecting adaptation of bacteria and fungi to decompose structural compounds in rainforest litter but not (or less) in rubber and oil palm litter. Bacterial and fungal community composition and testate amoeba species number and density varied strongly with litter type, but little with land use. However, community composition of testate amoebae was mainly affected by land use. Generally, changes in bacteria, fungi and testate amoebae were linked to changes in litter element concentrations, suggesting that element ratios of litter material as basal resource for the decomposer food web shape the structure of decomposer communities and decomposition processes via bottom-up forces. Overall, changing rainforest to monoculture plantations shifts the decomposer community structure and negatively affects litter decomposition.

A Lipid Extraction and Analysis Method for Characterizing Soil Microbes in Experiments with Many Samples

Microbial communities are important drivers and regulators of ecosystem processes. To understand how management of ecosystems may affect microbial communities, a relatively precise but effort-intensive technique to assay microbial community composition is phospholipid fatty acid (PLFA) analysis. PLFA was developed to analyze phospholipid biomarkers, which can be used as indicators of microbial biomass and the composition of broad functional groups of fungi and bacteria. It has commonly been used to compare soils under alternative plant communities, ecology, and management regimes. The PLFA method has been shown to be sensitive to detecting shifts in microbial community composition. An alternative method, fatty acid methyl ester extraction and analysis (MIDI-FA) was developed for rapid extraction of total lipids, without separation of the phospholipid fraction, from pure cultures as a microbial identification technique. This method is rapid but is less suited for soil samples because it lacks an initial step separating soil particles and begins instead with a saponification reaction that likely produces artifacts from the background organic matter in the soil. This article describes a method that increases throughput while balancing effort and accuracy for extraction of lipids from the cell membranes of microorganisms for use in characterizing both total lipids and the relative abundance of indicator lipids to determine soil microbial community structure in studies with many samples. The method combines the accuracy achieved through PLFA profiling by extracting and concentrating soil lipids as a first step, and a reduction in effort by saponifying the organic material extracted and processing with the MIDI-FA method as a second step.

Changes in Structure and Functioning of Protist (Testate Amoebae) Communities Due to Conversion of Lowland Rainforest into Rubber and Oil Palm Plantations

Large areas of tropical rainforest are being converted to agricultural and plantation land uses, but little is known of biodiversity and ecological functioning under these replacement land uses. We investigated the effects of conversion of rainforest into jungle rubber, intensive rubber and oil palm plantations on testate amoebae, diverse and functionally important protists in litter and soil. Living testate amoebae species richness, density and biomass were all lower in replacement land uses than in rainforest, with the impact being more pronounced in litter than in soil. Similar abundances of species of high and low trophic level in rainforest suggest that trophic interactions are more balanced, with a high number of functionally redundant species, than in rubber and oil palm. In contrast, plantations had a low density of high trophic level species indicating losses of functions. This was particularly so in oil palm plantations. In addition, the relative density of species with siliceous shells was >50% lower in the litter layer of oil palm and rubber compared to rainforest and jungle rubber. This difference suggests that rainforest conversion changes biogenic silicon pools and increases silicon losses. Overall, the lower species richness, density and biomass in plantations than in rainforest, and the changes in the functional composition of the testate amoebae community, indicate detrimental effects of rainforest conversion on the structure and functioning of microbial food webs.

Glyphosate herbicide affects belowground interactions between earthworms and symbiotic mycorrhizal fungi in a model ecosystem

Herbicides containing glyphosate are widely used in agriculture and private gardens, however, surprisingly little is known on potential side effects on non-target soil organisms. In a greenhouse experiment with white clover we investigated, to what extent a globally-used glyphosate herbicide affects interactions between essential soil organisms such as earthworms and arbuscular mycorrhizal fungi (AMF). We found that herbicides significantly decreased root mycorrhization, soil AMF spore biomass, vesicles and propagules. Herbicide application and earthworms increased soil hyphal biomass and tended to reduce soil water infiltration after a simulated heavy rainfall. Herbicide application in interaction with AMF led to slightly heavier but less active earthworms. Leaching of glyphosate after a simulated rainfall was substantial and altered by earthworms and AMF. These sizeable changes provide impetus for more general attention to side-effects of glyphosate-based herbicides on key soil organisms and their associated ecosystem services.