Shifts in soil microbial community structure, nitrogen cycling and the concomitant declining N availability in ageing primary boreal forest ecosystems

AbstractPlant growth in boreal forests is commonly limited by a low supply of nitrogen, a condition that may be aggravated by high tree below-ground allocation of carbon to ectomycorrhizal (ECM) fungi and associated microorganisms. These in turn immobilise N and reduce its availability to plants as boreal ecosystems develop. Here, we studied a boreal forest ecosystem chronosequence created by new land rising out of the sea due to iso-static rebound along the coast of northern Sweden. We used height over the ocean to estimate ecosystem age and examined its relationship to soil microbial community structure and the gross turnover of N. The youngest soils develop with meadows by the coast, followed by a zone of N2-fixing alder trees, and primary boreal conifer forest on ground up to 560 years old. The young soils in meadows contained little organic matter and microbial biomass per unit area. Nitrogen was turned over at low rates when expressed per area (m−2), but specific rates (per gram soil carbon (C)) were the highest found along the transect. In the zone with alder, the amounts of soil C and microbial biomass were much higher (bacterial biomass had doubled and fungal biomass quadrupled). Rates of gross N mineralisation (expressed on an area basis) were highest, but the retention of added labelled NH4+ was lowest in this soil as compared to other ages. The alder zone also had the largest extractable pools of inorganic N in soil and highest N % in plant foliage. In the older conifer forest ecosystems the amounts of soil C and N, as well as biomass of both bacteria and fungi increased. Data on organic matter 14C suggested that the largest input of recently fixed plant C occurred in the younger coniferous forest ecosystems. With increasing ecosystem age, the ratio of microbial C to total soil C was constant, whereas the ratio of microbial N to total soil N increased and gross N mineralization declined. Simultaneously, plant foliar N % decreased and the natural abundance of 15N in the soil increased. More specifically, the difference in δ15N between plant foliage and soil increased, which is related to relatively greater retention of 15N relative to 14N by ECM fungi as N is taken up from the soil and some N is transferred to the plant host. In the conifer forest, where these changes were greatest, we found increased fungal biomass in the F- and H-horizons of the mor-layer, in which ECM fungi are known to dominate (the uppermost horizon with litter and moss is dominated by saprotrophic fungi). Hence, we propose that the decreasing availability of N to the plants and the subsequent decline in plant production in ageing boreal forests is linked to high tree belowground C allocation to ECM fungi, a strong microbial sink for available soil N

Introducing GLUSEEN: A New Open Access and Experimental Network in Urban Soil Ecology

Peer reviewe

Metagenomics Reveals Bacterial and Archaeal Adaptation to Urban Land-Use : N Catabolism, Methanogenesis, and Nutrient Acquisition

Urbanization results in the systemic conversion of land-use, driving habitat and biodiversity loss. The "urban convergence hypothesis" posits that urbanization represents a merging of habitat characteristics, in turn driving physiological and functional responses within the biotic community. To test this hypothesis, we sampled five cities (Baltimore, MD, United States; Helsinki and Lahti, Finland; Budapest, Hungary; Potchefstroom, South Africa) across four different biomes. Within each city, we sampled four land-use categories that represented a gradient of increasing disturbance and management (from least intervention to highest disturbance: reference, remnant, turf/lawn, and ruderal). Previously, we used amplicon sequencing that targeted bacteria/archaea (16S rRNA) and fungi (ITS) and reported convergence in the archaeal community. Here, we applied shotgun metagenomic sequencing and QPCR of functional genes to the same soil DNA extracts to test convergence in microbial function. Our results suggest that urban land-use drives changes in gene abundance related to both the soil N and C metabolism. Our updated analysis found taxonomic convergence in both the archaeal and bacterial community (16S amplicon data). Convergence of the archaea was driven by increased abundance of ammonia oxidizing archaea and genes for ammonia oxidation (QPCR and shotgun metagenomics). The proliferation of ammonia-oxidizers under turf and ruderal land-use likely also contributes to the previously documented convergence of soil mineral N pools. We also found a higher relative abundance of methanogens (amplicon sequencing), a higher relative abundance of gene sequences putatively identified as Ni-Fe hydrogenase and nickel uptake (shotgun metagenomics) under urban land-use; and a convergence of gene sequences putatively identified as contributing to the nickel transport function under urban turf sites. High levels of disturbance lead to a higher relative abundance of gene sequences putatively identified as multiple antibiotic resistance protein marA and multidrug efflux pump mexD, but did not lead to an overall convergence in antibiotic resistance gene sequences.Peer reviewe

Soil microbial communities in diverse agroecosystems exposed to the herbicide glyphosate

© 2020 American Society for Microbiology. Despite glyphosate\u27s wide use for weed control in agriculture, questions remain about the herbicide\u27s effect on soil microbial communities. The existing scientific literature contains conflicting results, from no observable effect of glyphosate to the enrichment of agricultural pathogens such as Fusarium spp. We conducted a comprehensive field-based study to compare the microbial communities on the roots of plants that received a foliar application of glyphosate to adjacent plants that did not. The 2-year study was conducted in Beltsville, MD, and Stoneville, MS, with corn and soybean crops grown in a variety of organic and conventional farming systems. By sequencing environmental metabarcode amplicons, the prokaryotic and fungal communities were described, along with chemical and physical properties of the soil. Sections of corn and soybean roots were plated to screen for the presence of plant pathogens. Geography, farming system, and season were significant factors determining the composition of fungal and prokaryotic communities. Plots treated with glyphosate did not differ from untreated plots in overall microbial community composition after controlling for other factors. We did not detect an effect of glyphosate treatment on the relative abundance of organisms such as Fusarium spp

Earthworm assemblages in urban habitats across biogeographical regions

In urban landscapes, humans are the most significant factor determining belowground diversity, including earthworms. Within the framework of the Global Urban Soil Ecology and Education Network (GLUSEEN), a multi-city comparison was carried out to assess the effects of soil disturbance on earthworms. In each of five cities (Baltimore, USA; Budapest, Hungary; Helsinki and Lahti, Finland; Potchefstroom, South Africa), covering four climatic and biogeographical regions, four habitat types (ruderal, turf/lawn, remnant and reference) were sampled. The survey resulted in 19 species belonging to 9 genera and 4 families. The highest total species richness was recorded in Baltimore (16), while Budapest and the Finnish cities had relatively low (5–6) species numbers. Remnant forests and lawns supported the highest earthworm biomass. Soil properties (i.e. pH and organic matter content) explained neither earthworm community composition nor abundance. Evaluating all cities together, earthworm communities were significantly structured by habitat type. Communities in the two adjacent cities, Helsinki and Lahti were very similar, but Budapest clearly separated from the Finnish cities. Earthworm community structure in Baltimore overlapped with that of the other cities. Despite differences in climate, soils and biogeography among the cities, earthworm communities were highly similar within the urban habitat types. This indicates that human-mediated dispersal is an important factor shaping the urban fauna, both at local and regional scales.Peer reviewe

Előzetes eredmények városi talajok lebontó hatásfokának vizsgálatáról (GLUSEEN-Projekt, Budapest)

A „Global Urban Soil Ecology and Education” hálózat előkészítő kutatása második éve folyik – a világ 4 régiójának 5 helyszínén –, Magyarország részvételével. A kutatás célja az ún. „konvergencia hipotézis” tesztelése különböző minőségű/zavartságú városi talajok szerves anyag lebontási hatásfokán keresztül. A konvergencia hipotézis szerint a természetes ökoszisztémák az urbanizáció hatására hasonló irányú változást mutatnak globális szinten. A cél mind tudományos igényű kutatások, mind az érdeklődő lakosság bevonására alkalmas egyszerű, könnyen kivitelezhető, költséghatékony módszerek kidolgozása, tesztelése. A kutatás során 4 élőhelytípust (5–5 ismétlésben) jelöltünk ki: 1) erősen zavart (ruderális), 2) városi gyep, 3) az urbanizáció eredményeként fragmentálódott erdőfoltok és 4) referenciaként szolgáló természetközeli erdők területei. A szervesanyag bomlásának mértékét 2013-ban leásott teafilterekkel vizsgáltuk, amelyeket 4, 6, 10, 12 hónap után gyűjtöttünk vissza. Eredményeink szerint a 6. hónaptól szignifikáns különbség mutatkozott az élőhelytípusok között a lebontási sebességben (F = 11,238; p < 0,0001), ami a városi gyepeken és ruderális élőhelyeken volt a legnagyobb. Ez összhangban van a többi 4 városban kapott eredménnyel, ami alátámasztja a konvergencia hipotézist: a különböző éghajlatú, alapkőzetű talajok kémhatása és humusztartalma az erősen zavart és városi gyep élőhelyek esetén azonos irányú változást mutatnak világszerte

The successes and challenges of harmonising juvenile idiopathic arthritis (JIA) datasets to create a large-scale JIA data resource

Background CLUSTER is a UK consortium focussed on precision medicine research in JIA/JIA-Uveitis. As part of this programme, a large-scale JIA data resource was created by harmonizing and pooling existing real-world studies. Here we present challenges and progress towards creation of this unique large JIA dataset. Methods Four real-world studies contributed data; two clinical datasets of JIA patients starting first-line methotrexate (MTX) or tumour necrosis factor inhibitors (TNFi) were created. Variables were selected based on a previously developed core dataset, and encrypted NHS numbers were used to identify children contributing similar data across multiple studies. Results Of 7013 records (from 5435 individuals), 2882 (1304 individuals) represented the same child across studies. The final datasets contain 2899 (MTX) and 2401 (TNFi) unique patients; 1018 are in both datasets. Missingness ranged from 10 to 60% and was not improved through harmonisation. Conclusions Combining data across studies has achieved dataset sizes rarely seen in JIA, invaluable to progressing research. Losing variable specificity and missingness, and their impact on future analyses requires further consideration

Agricultural practices influence foliar endophytic communities in coffee plants of different varieties

Abstract Fungal endophytes are pivotal components of a plant's microbiome, profoundly impacting its health and fitness. Yet, myriad questions remain concerning the intricate interactions between these microorganisms and their hosts, particularly in the context of agriculturally important plants such as Coffea arabica. To bridge this knowledge gap and provide a comprehensive framework, this study investigated how farming practices shape the taxonomic and functional diversity of phylloplane endophytes in coffee. Coffee plant leaves from two distinct producing regions in Costa Rica were sampled, ensuring the representation of various coffee varieties (Obatá, Catuaí, and Caturra), agricultural management methods (organic vs. conventional), sun exposure regimes (full sunlight/monoculture vs. natural shade/agroforestry), and leaf developmental stages (newly emerged asymptomatic vs. mature leaves). Fungal communities were characterized by employing both culture‐dependent and independent techniques (internal transcribed spacer 2 nuclear ribosomal DNA metabarcoding). The results showed a greater diversity of endophytes in mature leaves and conventionally managed plants, with coffee variety exerting an unclear influence. The effect of sun exposure was surprisingly negligible. However, data emphasize the benefits of agroforestry and organic farming, which are linked to reduced putative pathogens and heightened levels of potentially mutualistic fungi, fostering functionally diverse communities. Despite the role that plant microbiomes might play in agricultural production, the knowledge to shape endophytic communities through breeding or management is lacking. The results from this study provide a framework to understand how both plant and agricultural practices influence endophyte diversity within coffee crops. These insights hold promise for guiding future efforts to manipulate coffee microbial communities effectively

The Role of Tire Leachate in Condition-Specific Competition and the Persistence of a Resident Mosquito from a Competitively Superior Invader

(1) Background: Condition-specific competition, when the outcome of competition varies with abiotic conditions, can facilitate species coexistence in spatially or temporally variable environments. Discarded vehicle tires degrade to leach contaminants into collected rainwater that provide habitats for competing mosquito species. We tested the hypothesis that more highly degraded tires that contain greater tire leachate alters interspecific mosquito competition to produce a condition-specific advantage for the resident, Culex pipiens, by altering the outcome of competition with the competitively superior invasive Aedes albopictus. (2) Methods: In a competition trial, varying densities of newly hatched Ae. albopictus and Cx. pipiens larvae were added to tires that had been exposed to three different ultraviolet (UV)-B conditions that mimicked full-sun, shade, or no UV-B conditions in the field. We also measured Cx. pipiens and Ae. albopictus oviposition preference among four treatments with varying tire leachate (high and low) and resources (high and low) amounts to determine if adult gravid females avoided habitats with higher tire leachate. (3) Results: We found stronger competitive effects of Cx. pipiens on the population performance and survival of Ae. albopictus in tires exposed to shade and full-sun conditions that had higher concentrations of contaminants. Further, zinc concentration was higher in emergent adults of Ae. albopictus than Cx. pipiens. Oviposition by these species was similar between tire leachate treatments but not by resource amount. (4) Conclusions: These results suggest that degraded tires with higher tire leachate may promote condition-specific competition by reducing the competitive advantage of invasive Ae. albopictus over resident Cx. pipiens and, combined with Cx. pipiens’ preferential oviposition in higher resource sites, contribute to the persistence of the resident species

Urbanization Altered Bacterial and Archaeal Composition in Tidal Freshwater Wetlands Near Washington DC, USA, and Buenos Aires, Argentina

Urban expansion causes coastal wetland loss, and environmental stressors associated with development can lead to wetland degradation and loss of ecosystem services. This study investigated the effect of urbanization on prokaryotic community composition in tidal freshwater wetlands. Sites in an urban, suburban, and rural setting were located near Buenos Aires, Argentina, and Washington D.C., USA. We sampled soil associated with two pairs of functionally similar plant species, and used Illumina sequencing of the 16S rRNA gene to examine changes in prokaryotic communities. Urban stressors included raw sewage inputs, nutrient pollution, and polycyclic aromatic hydrocarbons. Prokaryotic communities changed along the gradient (nested PerMANOVA, Buenos Aires: p = 0.005; Washington D.C.: p = 0.001), but did not differ between plant species within sites. Indicator taxa included Methanobacteria in rural sites, and nitrifying bacteria in urban sites, and we observed a decrease in methanogens and an increase in ammonia-oxidizers from rural to urban sites. Functional profiles in the Buenos Aires communities showed higher abundance of pathways related to nitrification and xenobiotic degradation in the urban site. These results suggest that changes in prokaryotic taxa across the gradient were due to surrounding stressors, and communities in urban and rural wetlands are likely carrying out different functions