Chronic nitrogen deposition and the composition of active arbuscular mycorrhizal fungi

A growing body of evidence indicates that atmospheric nitrogen (N) deposition can alter the composition and function of arbuscular mycorrhizal fungi (AMF) associated with plant roots. We studied the community of AMF actively transcribing ribosomal genes in the forest floor of northern hardwood forests dominated by sugar maple (Acer saccharum Marsh.) that have been exposed to experimental N deposition since 1994 (30 kg NO₃⁻-N ha⁻¹ year⁻¹). Our objective was to evaluate whether previously observed declines in AM root infection and mycelial production resulted in a compositional shift in the AM fungi actively providing resources to plant symbionts under chronic N deposition. To accomplish this task, we cloned and sequenced the LSU of reverse-transcribed AM fungal rRNA extracted from the forest floor under ambient and experimental N deposition treatments. We found that experimental N deposition did not alter the active community of AMF or AMF diversity, but we did observe a significant decrease in rare taxa under chronic N deposition. Our results indicate that chronic N deposition, at levels expected by the end of this century, can exert a moderate influence on the composition and abundance of AMF associated with plant roots in a wide-spread forest ecosystem in the northeastern North America.     

Global food security,biodiversity conservation and the future of agricultural intensification

There is vigorous debate about the potential for reforestation to offset losses in biodiversity associated with tropical deforestation, but a scarcity of good data. We quantified developmental trajectories following active restoration (replanting) of deforested pasture land to tropical Australian rainforest, using 20 different bird community indicators within chronosequences of multiple sites. Bird species composition in restored sites (1–24 years old) was intermediate between that of reference sites in pasture and primary rainforest. Total species richness was much less sensitive to land cover change than composition indicators, because of contrasting species-specific response patterns. For example, open-country (grassland/wetland) bird species declined in richness and abundance with increasing site age, while rainforest-dependent species increased. Results from two different landscapes (uplands and lowlands) were remarkably consistent, despite differing bird assemblages. After 10 years, restored sites averaged about half the number of rainforest-dependent bird species typical of rainforest. Mean values at around 20 years overlapped with the “poorest” rainforest reference sites, but projections suggest that >150 years are required to reach mean rainforest levels, and high variability among sites means that many were not on track towards ever achieving a rainforest-like bird community. Regional rainforest endemics were half as likely to occupy older revegetated sites as non-endemic rainforest-dependent species. Between-site variability and slow colonisation by regional endemics strongly constrain the potential of rainforest restoration to offset the biodiversity impacts of tropical deforestation. The results also mean that ongoing monitoring of biodiversity is an essential part of restoration management.     

Temporal variation outweighs effects of biosolids applications in shaping arbuscular mycorrhizal fungi communities on plants grown in pasture and arable soils

Landspreading of biosolids (treated sewage sludge) in agroecosystems is a common waste management practice worldwide. Evidence suggests biosolids may be detrimental to arbuscular mycorrhizal fungi (AMF); however, previous studies focused on arable systems and often unrealistically high biosolids application levels. We investigated the effects of biosolids on AMF communities in grassland and arable agroecosystems, in the context of the natural seasonal dynamics of AMF community composition and diversity. A pasture and arable system under commercial farming management were amended annually with two different types of biosolids, applied at levels meeting current European Union regulations, in a factorial, replicated field-scale plot experiment. AMF root colonisation and community composition were measured in Lolium perenne roots from the pasture and Trifolium repens roots growing in arable soil across the seasons of two years. AMF community compositions were assessed by terminal-restriction fragment length polymorphism analyses. Biosolids had no significant effect on AMF root colonisation or community composition in either agroecosystem. Soil chemical analyses indicated several changes in the top 0–5 cm layer of the pasture soil, including small increases in heavy metal concentrations in biosolids relative to control plots. Temporal AMF dynamics were detected in soils from both agroecosystem indicating that the effect of seasonality outweighed that of biosolids application.     

Land use influences soil fungal community composition across central Victoria,south-eastern Australia

Current theory expects that fungi, on the one hand, are spatially ubiquitous but, on the other, are more susceptible than bacteria to disturbance such as land use change due to dispersal limitations. This study examined the relative importance of location and land use effects in determining soil fungal community composition in south-eastern Australia. We use terminal restriction fragment length polymorphism (T-RFLP; primer pair ITS1-F–ITS4) and multivariate statistical methods (NMDS ordinations, ANOSIM tests) to compare relative similarities of soil fungal communities from nine sites encompassing three locations (ca 50–200 km apart) and four land uses (native eucalypt forest, Pinus radiata plantation, Eucalyptus globulus plantation, and unimproved pasture). Location effects were generally weak (e.g. ANOSIM test statistic R ≤ 0.49) and were, in part, attributed to minor differences in soil texture. By contrast, we found clear and consistent evidence of land use effects on soil fungal community composition (R ≤ 0.95). That is, soils from sites of the same land use grouped together in NMDS ordinations of fungal composition despite geographic separations of up to ca 175 km (native eucalypt forests) and 215 km (P. radiata plantations). In addition, different land uses from the same location were clearly separate in NMDS ordinations, despite, in one case, being just 180 m apart and having similar land use histories (i.e. P. radiata versus E. globulus plantation both established on pasture in the previous decade). Given negligible management of all sites beyond the early establishment phase, we attribute much of the land use effects to changes in dominant plant species based on consistent evidence elsewhere of strong specificity in pine and eucalypt mycorrhizal associations. In addition, weak to moderate correlations between soil fungal community composition and soil chemical variables (e.g. Spearman rank correlation coefficients for individual variables of 0.08–0.32), indicated a minor contributing role of vegetation-mediated changes in litter and soil chemistry. Our data provide evidence of considerable plasticity in soil fungal community composition over time spans as short as 6–11 years. This suggests that – at least within geographic zones characterised by more-or-less contiguous forest cover – soil fungal community composition depends most on availability of suitable habitat because dispersal propagules are readily available for colonisation after land use change.     

Transient elevation of carbon dioxide modifies the microbial community composition in a semi-arid grassland

Using open-top chambers (OTC) on the shortgrass steppe in northern Colorado, changes of microbial community composition were followed over the latter 3 years of a 5-year study of elevated atmospheric CO₂ as well as during 12 months after CO₂ amendment ended. The experiment was composed of nine experimental plots: three chambered plots maintained at ambient CO₂ levels of 360±20 μmol mol^?1 (ambient treatment), three chambered plots maintained at 720±20 μmol mol^?1 CO₂ (elevated treatment) and three unchambered plots. The abundance of fungal phospholipid fatty acids (PLFAs) shifted in the shortgrass steppe under the influence of elevation of CO₂ over the period of 3 years. Whereas the content of the fungal signature molecule (18:2ω6) was similar in soils of the ambient and elevated treatments in the third year of the experiment, CO₂ treatment increased the content of 18:2ω6 by around 60% during the two subsequent years. The shift of microbial community composition towards a more fungal dominated community was likely due to slowly changing substrate quality; plant community forage quality declined under elevated CO₂ because of a decline of N in all tested species as well as shift in species composition towards greater abundance of the low forage quality species (Stipa comata). In the year after which CO₂ enrichment had ceased, abundances of fungal and bacterial PLFAs in the post-CO₂ treatment plots shifted slowly back towards the control plots. Therefore, quantity and quality of available substrates had not changed sufficiently to shift the microbial community permanently to a fungal dominated community. We conclude from PLFA composition of soil microorganisms during the CO₂ elevation experiment and during the subsequent year after cessation of CO₂ treatment that a shift towards a fungal dominated system under higher CO₂ concentrations may slow down C cycling in soils and therefore enhance C sequestration in the shortgrass steppe in future CO₂-enriched atmospheres.     

Recovery of woody plant diversity in tropical rain forests in southern China after logging and shifting cultivation

Logging and intense shifting cultivation have caused major degradation of tropical forests and loss of biodiversity. Understanding the direct and indirect effects of those land uses on plant biodiversity is essential to the restoration of tropical forests. We compared the species diversity, community composition and basal area of all stems ?1 cm dbh among 18 1-ha tropical lowland and montane rain forest plots with a well-recorded long-term history of shifting cultivation and logging on Hainan Island, south China. We also explored the relative importance of disturbance and environmental factors in determining forest recovery. We found that the species density and diversity in old growth forests were higher than in shifting cultivation fallows (55 years old) but lower than in logged forests (35–40 years since logging). The species composition of shifting cultivation fallows was distinct from other forest types but logged forests were similar to old growth forests, especially in lowland forests. Disturbance intensity was the most frequently important factor in determining species composition, species density, diversity, and basal area accumulation. Soil nutrient availability explained some of the variation in species composition and diversity. Stem density was related to multiple factors including disturbance history, soil nutrients, and distance to old-growth forest. In general, we found that disturbance intensity was a better predictor of forest structure and diversity than edaphic environmental variables, highlighting the importance of human impacts in shaping tropical forest successional pathways.     

Temporal variation of soil compaction and deterioration of soil quality in pasture areas of Colombian Amazonia

In the Amazon basin, tropical rainforest is being slashed and burned at accelerated rates for annual crops over a couple of years, followed by forage grasses. Because of poor management, the productivity of established pastures declines in a few years so that grazing plots are abandoned and new areas are deforested. Previous studies in the region report higher bulk density in soils under pasture than in similar soils under forest. The objective of this study was to detect changes in the physical quality of the topsoil of nutrient-poor Typic Paleudults in the colonisation area of Guaviare, Colombian Amazonia, and analyse the effect of soil deterioration on pasture performance. Temporal variation of soil compaction under pasture was analysed by comparing natural forest taken as control and pasture plots of Brachiaria decumbens (Stapf) grouped into three age ranges (<3, 3–9, >9 years). Evidence of soil compaction through cattle trampling, after clearing the primary forest, included the formation of an Ap horizon with platy structure and dominant greyish or olive colours, reflecting impaired surface drainage, the increase of bulk density and penetration resistance, and the decrease of porosity and infiltration rate. From primary forest to pastures older than 9 years, bulk density of the 5–10 cm layer increase was 42% in fine-textured soils and 30% in coarse-textured soils. Penetration resistance ranged from 0.45 MPa under forest to 4.25 MPa in old pastures, with maximum values occurring at 3–12 cm depth in pastures older than 9 years. Average total soil porosity was 58–62% under forest and 46–49% under pasture. Basic infiltration dropped from 15 cm h⁻¹ in the original forest conditions to less than 1 cm h⁻¹ in old pastures. Crude protein content and dry matter yield of the forage grass steadily decreased over time. No clear relationship between declining protein content as a function of pasture age and changes in chemical soil properties was found, but there was a high negative correlation (r=−0.81) between protein content and bulk density, reflecting the effect of soil compaction on pasture performance. After about 9–10 years of use, established grass did no longer compete successfully with invading weeds and grazing plots were abandoned. As land is not yet a scarcity in this colonisation area, degraded pastures are seldom rehabilitated.     

Beetles community structures under different reclamation practices

Differences in beetle community structures between not re-cultivated over 60 years old forest and 10 years old re-cultivated meadow and shrubs were compared. On each locality there were arranged three replicates of 10 pitfall trap rows. Mean abundance of beetles was significantly greater on old forest stand than re-cultivated meadow. However no significant differences between localities in species richness and non parametric index of diversity (Shannon H′) were recorded. Rank–abundance curves for newly established communities best fits to geometric model of distribution (r = 0.98, P < 0.001) which is characteristic for species poor communities, where a single environmental resource is extremely important, meanwhile old stand, without any reclamation practice is best fitted to lognormal distribution model (r = 0.99, P < 0.001) which is typical for more stable and well developed communities. Principal component analysis for log (N + 1) transformed matrix of abundances described well 60% of the total variance. Two clear groups of species transects were derived: one concentrated assemblages of both reclaimed and newly established communities and the second one old non reclaimed forest stands. Significant feature of trophic guild structure in all three communities is the lowest abundance of decomposers meanwhile predators predominate on non re-cultivated old sites and herbivores on reclaimed young stands.     

Recovery of amphibian species richness and composition in a chronosequence of secondary forests,northeastern Costa Rica

In some tropical regions, following the abandonment of agriculture and pastures, secondary forests can recover plant species richness and forest structure (e.g. canopy cover, biomass); however, the importance of these secondary forests for fauna is not clear. Secondary forests can benefit fauna by providing suitable habitats, connecting forests fragments, and increasing gene flow. Previous studies of forest regeneration have showed different levels of amphibian recovery. In Puerto Rico, 1–5 years old secondary forests achieved similar amphibian species richness and composition in comparison with old-growth forests, while in Brazil secondary forests from 14 to 19 years of recovery only recovered 60% of the species of old-growth forests. We evaluated amphibian recovery in secondary forests in northeastern Costa Rica, by assessing amphibian recovery in 12 secondary forests that vary in age of recovery and in three old-growth forests using visual and acoustic surveys. Our sites varied in terms of their landscape (e.g. amount of surrounding forest) and forest characteristics (e.g. forest age, aboveground biomass, basal area, number of tree species, number of stems, leaf-litter depth), but there was no relationship between these characteristics and amphibian species richness or species composition. We found that amphibians are recovering rapidly in secondary forests in Costa Rica, and even young forests (10–16 years) had similar species richness and composition in comparison with old-growth forests. These forests are providing suitable microhabitats conditions for amphibians. In addition, this study highlights the importance of landscape characteristics. The abundance of amphibian species sources (e.g. forest patches) and connections between forests appear to be helping the species colonize these sites. Worldwide, the area of secondary forests is increasing, and our results show that these habitats are suitable for a diversity of amphibian species, suggesting that these forests can help reduce amphibian population and species decline.     

The effects of mixed broad-leaved trees on the collembolan community in larch plantations of central Japan

The effects of broad-leaved trees on the collembolan community in larch plantations were investigated at the foot of Mt. Yatsugatake (1200–1400 m a.s.l.) in Japan. The study sites comprised five pure larch plantation plots (larch dominated more than 95% of the area at breast height) and five mixed forest plots (larch dominated between 50% and 80% of the area at breast height). We compared the collembolan community structures between stand types and related them to the plant community composition and soil properties at each plot. Density and species richness of Collembola were not significantly different between pure larch and mixed plots. Using partial redundancy analysis (pRDA), the variance of collembolan species data in the litter layer was explained by the biomass of grass on the forest floor, and the variance in the soil layer was explained by the biomass of total forest floor plants. These results suggest that the biomass or the composition of forest floor plants influence the collembolan community more than the crown trees in this area.     

Earthworms as soil quality indicators in Brazilian no-tillage systems

It is well known that earthworm populations tend to increase under no-tillage (NT) practices, but abundances tend to be highly variable. In the present study, data from the literature together with those on earthworm populations sampled in six watersheds in SW Paraná State, Brazil, were used to build a classification of the biological soil quality of NT systems based on earthworm density and species richness. Earthworms were collected in 34 farms with NT aging from 3 to 27 yr, in February 2010, using an adaptation of the TSBF (Tropical Soil Biology and Fertility) Program method (hand sorting of five 20 cm × 20 cm holes to 20 cm depth). Six forest sites were also sampled in order to compare abundances and species richness with the NT systems. Species richness in the 34 NT sites and in the 6 forests ranged from 1 to 6 species. Most earthworms encountered were exotics belonging to the genus Dichogaster (D. saliens, D. gracilis, D. bolaui and D. affinis) and native Ocnerodrilidae (mainly Belladrilus sp.), all of small individual size. In a few sites, individuals of the Glossoscolecidae (P. corethrurus, Glossoscolex sp., Fimoscolex sp.) and Megascolecidae (Amynthas gracilis) families were also encountered, in low densities. Urobenus brasiliensis (Glossoscolecidae) were found only in the forest fragments. In the NT farms, earthworm abundance ranged from 5 to 605 ind m⁻² and in the forest sites, from 10 to 285 ind m⁻². The ranking of the NT soil biological quality, based on earthworm abundance and species richness was: poor, with <25 individuals per m⁻² and 1 sp.; moderate, with ≥25–100 individuals per m⁻² and 2–3 sp.; good, with >100–200 individuals per m⁻² and 4–5 sp.; excellent, with >200 individuals per m⁻² and >6 sp. About 60% of the 34 farms fell into the poor to moderate categories based on this classification, so further improvements to the NT farm's management system are needed to enhance earthworm populations. Nevertheless, further validation of this ranking system is necessary to allow for its wider-spread use.     

Do boundaries of soil animal and plant communities coincide? A case study of a Mediterranean forest in Russia

We studied the relationship between plant and soil animal communities by geostatistical analysis in a piedmont forest close to Novorossiysk (Southern Russia). Vegetation on the slope of a hill was an oak-ash-hornbeam forest, while the vegetation on the foot of the hill was a maple-ash-hornbeam forest. Two plots were studied each including both slope and foot habitats. On every plot samples collected formed a grid of 10 × 5 units with a 5 m distance between them. Soil macroinvertebrates were hand-sorted from the samples, and several soil parameters (soil, pebble, and litter mass, soil moisture) were measured.The analysis did not reveal coincidence between the boundaries of plant and soil animal communities on the bend of the hill. Soil animal communities of the plots were dominated by woodlice, diplopods, and insect larvae, reaching an abundance of 680–990 individuals m⁻² throughout the plots. Number of taxonomic groups per sample and overall animal abundance in the bend were the highest in both plots, whilst these parameters on the slope were the lowest. Variograms and maps of spatial distribution indicated that the boundary between soil animal communities was situated further up on the slope than the vegetation boundary. The size of the animal community was smaller than the size of plots sampled, what probably explained the lack of coincidence between the boundaries. There was a significant correlation between distribution of litter mass and parameters of soil animal communities, which was modulated by depth of soil layer and soil moisture. Soil parameters were more important for explaining boundaries between soil animal communities than plant communities in the forest considered.     

Influences of non-herbaceous biochar on arbuscular mycorrhizal fungal abundances in roots and soils: Results from growth-chamber and field experiments

Biochar holds promise as an amendment for soil quality improvement and sequestration of atmospheric carbon dioxide. However, knowledge of how biochar influences soil properties, especially soil microorganisms, is limited. Three separate studies were conducted, with two studies using Plantago lanceolata as the AMF hosting plant, and a third being conducted in the field. Each of the three studies employed a different soil type. Furthermore, a total of five different biochars, and ten different biochar application rates, were used across the three experiments. All experiments had the goal to examine biochar influences on arbuscular mycorrhizal fungal (AMF) abundance in roots and AMF abundance (hyphal lengths) in soils. AMF abundance was either decreased or remained unchanged across all biochar treatments. When AMF abundances decreased, significant changes in soil properties, primarily in soil P availability, were observed. Application of large quantities (2.0% and 4.0%, w/w) of a lodgepole pine biochar, led to significant declines in AMF abundance in roots of 58% and 73% respectively, but not in soils. These declines in AMF abundance were accompanied by significant declines (28% and 34%) in soil P availability. After addition of a peanut shell biochar produced at 360 °C, P increased by 101% while AMF root colonization and extraradical hyphal lengths deceased by 74% and 95% respectively. Field application of mango wood biochar at rates of 23.2 and 116.1 t C ha⁻¹ increased P availabilities by 163% and 208% respectively and decreased AMF abundances in soils by 43% and 77%. These findings may have implications for soil management where the goal is to increase the services provided by AMF.     

Tillage and slurry over-fertilization affect oribatid mite communities in a semiarid Mediterranean environment

Fertilization with animal residues together with no-tillage is being widely used in dryland Mediterranean agriculture. The aim of this work is to assess the potential impacts of these combined management practices on oribatid mite species, and to evaluate their potential use as bioindicators of soil disturbances. From an experiment established ten years ago, eight fertilization treatments (including minerals or pig slurries), all combined with minimum tillage (MT) and no-tillage (NT), were studied. Four of these combinations were sampled three times during the winter cereal cropping season. The rest, and a neighbouring oak forest, were only sampled close to the end of the season (May). In total, 34 oribatid species and 4140 individuals were recovered. Oribatid abundance responded positively (p < 0.05) to the reduction of tillage intensity (NT) and marginally (p < 0.1) to slurry fertilization at sowing (close to maximum legislation allowed rate: <210 kg N ha⁻¹ yr⁻¹). At this slurry rate, Shannon index of diversity varied through the season, and was higher in May in MT than in NT plots. The Berger–Parker index of abundance signals plots without slurries as the most disturbed (compared with the forest). Nitrogen slurry over-fertilization reduced abundance of Oribatula (Zygoribatula) connexa connexa , but the impact on the most relevant species depended on the tillage system: Epilohmannia cylindrica cylindrica dominated in MT plots; under NT it was balanced by Tectocepheus velatus sarekensis and Passalozetes (Passalozetes) africanus. Scutovertex sculptus is also very negatively affected by tillage. Oribatida are a good target for the biological indication of soil disturbances associated to agricultural management.     

Interactions between plant species and mycorrhizal colonization on the bacterial community composition in the rhizosphere

This study assessed the effect of mycorrhizal colonization by Glomus intraradices (Gi) and G. versiforme (Gv) on the bacterial community composition in the rhizosphere of canola, clover and two tomato genotypes (wild type (76R) and its mutant with reduced mycorrhizal colonization (rmc)). Additionally, the effect of light intensity on the rhizosphere bacterial community composition of the tomato genotypes was studied. The bacterial community composition was assessed by denaturing gradient gel electrophoresis (DGGE). In canola, which is considered to be a non-mycorrhizal species, inoculation with Gi increased the shoot dw compared to Gv and the non-mycorrhizal control plants and also induced changes in the bacterial community composition in the rhizosphere. These fungal effects were observed although less than 8% of the root length of canola was colonized. On the other hand, about 50% of the root length of clover was colonized and inoculation with Gv resulted in a higher shoot dw compared to Gi or the control plants but the rhizosphere bacterial community composition was not affected by inoculation. Plant growth, mycorrhizal colonization and bacterial community composition of the two tomato genotypes were affected by a complex interaction between tomato genotype, AM fungal species and light intensity. Low light intensity (photosynthetic photon flux 200–250 μmol m⁻² s⁻¹) increased the shoot–root ratio in both genotypes and reduced colonization in the wild type. The differences in bacterial community composition between the two genotypes were more pronounced at low than at high light intensity (550–650 μmol m⁻² s⁻¹).     

Biodiversity of arbuscular mycorrhizas in three vegetational types from the semiarid of Ceará State,Brazil

Semiarid lands are the object of a limited number of studies, very few among them aimed at characterizing root-associated fungal communities. The diverse vegetation occurring in the tropical dry forest from the Ceará State, Brazil, core area of the Brazilian tropical semiarid, has been attributed to its soil, topography and climatic variation. However, the arbuscular mycorrhizal (AM) symbiosis may have an important role in the function of these ecosystems. We examined AM association in 29 semiarid Brazilian species from three different locations: thorny dry woody savanna vegetation, known as caatinga; non-thorny dry forest and closed, non thorny dry tall-shrubby vegetation, known as carrasco. AM fungal diversity was also compared among the different sites. Twenty of the 22 trees and two of the seven herbs examined had AM association. Arum-type AM morphology was the dominant association occurring in 19 trees and in 3 hemicryptophyte plants. AM morphology is reported for the first time in 21 trees and two herbaceous species. Over the different sites, spore densities in the soil ranged from 5 to 32 per 100 g air-dried soil. Spores of 32 AM fungal taxa were isolated from the soil samples of trees of which twelve belonged to Acaulospora, two to Scutellospora, three to Gigaspora, four to Racocetra, three to Glomus, one to Clareoideoglomus, one to Ambispora, one to Pacispora, one to Sclerocystis, one to Dentiscutata, one to Orbispora, one to Quatunica and one to Entrophospora. Species richness was high in woody caatinga and Glomus macrocarpum, Gigaspora gigantea and Cetraspora pellucida were the most frequent species at different sites. Species diversity (Shannon–Weaver index) did not differ significantly among sites. Water content and phosphorus availability was found to influence the AMF species composition at the plant community level, providing information about the caatinga dominium biodiversity, mainly for its conservation.     

Arbuscular mycorrhizal fungi are directly and indirectly affected by glyphosate application

Glyphosate is a systemic non-selective herbicide, the most widely used in the world. Alongside with its use in agricultural and forestry systems, this herbicide is used in grasslands in late summer with the aim of promoting winter species with the consequent increase in stocking rate. However, its effects on non-target organisms, such as arbuscular mycorrhizal fungi (AMF), are unclear. Arbuscular mycorrhizal fungi (AMF) colonize the root of more than 80% of terrestrial plants, improving their growth and survival, and therefore playing a key role in ecosystem structure and function. The aim of this work was to investigate the possible pathways through which glyphosate application affects AMF spores viability and root colonization in grassland communities. Our hypothesis is that glyphosate application can damage AMF directly (through contact with spores and external hyphae) or indirectly through the changes it generates on host plants. The experiment had a factorial array with three factors: (1) plant species, at two levels (Paspalum dilatatum and Lotus tenuis), (2) doses of glyphosate, at three levels (0 l ha⁻¹, 0.8 l ha⁻¹ and 3 l ha ⁻¹), and (3) application site, at two levels: soil (direct pathway) and plant foliage (indirect pathway). Spore viability was reduced even under the lowest glyphosate rate, but only when it was applied on the soil. Total root colonization for both species was similarly decreased when glyphosate was applied to plant foliage or on soil, with no difference between 0.8 and 3 l ha⁻¹. The number of arbuscules was 20% lower when glyphosate was applied on plant foliage, than when it was applied on the soil. Our findings illustrate that glyphosate application negatively affects AMF functionality in grasslands, due to different causes depending on the herbicide application site. While, under field conditions, the occurrence of direct and/or indirect pathways will depend on the plant cover at the time of glyphosate application, the consequences of this practice on the plant community structure will vary with the mycorrhizal dependence of the species composition regardless of the pathway involved.     

Tag-encoded pyrosequencing analysis of bacterial diversity in a single soil type as affected by management and land use

Impacts of management and land use on soil bacterial diversity have not been well documented. Here we present the application of the bacterial tag encoded FLX amplicon pyrosequencing (bTEFAP) diversity method, which will promote studies in soil microbiomes. Using this modified FLX pyrosequencing approach we evaluated bacterial diversity of a soil (Pullman soil; fine, mixed, thermic Torrertic Paleustolls) with 38% clay and 34% sand (0–5 cm) under four systems. Two non-disturbed grass systems were evaluated including a pasture monoculture (Bothriochloa bladhii (Retz) S.T. Blake) [P] and a diverse mixture of grasses in the Conservation Reserve Program (CRP). Two agricultural systems were evaluated including a cotton (Gossypium hirsutum L.) -winter wheat (Triticum aestivum L.)-corn (Zea mays L.) rotation [Ct–W–Cr] and the typical practice of the region, which is continuous monoculture cotton (Ct–Ct). Differences due to land use and management were observed in soil microbial biomass C (CRP > P = Ct–W–Cr > Ct–Ct). Using three estimators of diversity, the maximum number of unique sequences operational taxonomic units (OTU; roughly corresponding to the species level) never exceeded 4500 in these soils at the 3% dissimilarity level. The following trend was found using the most common estimators of bacterial diversity: Ct–W–Cr > P = CRP > Ct–Ct. Predominant phyla in this soil were Actinobacteria, Bacteriodetes and Fermicutes. Bacteriodetes were more predominant in soil under agricultural systems (Ct–W–Cr and Ct–Ct) compared to the same soil under non-disturbed grass systems (P and CRP). The opposite trend was found for the Actinobacteria, which were more predominant under non-disturbed grass systems (P and CRP). Higher G? bacteria and lower G+ bacteria were found under Ct–W–Cr rotation and highest abundance of actinomycetes under CRP. The bTEFAP technique proved to be a powerful method to characterize the bacterial diversity of the soil studied under different management and land use in terms not only on the presence or absence, but also in terms of distribution.     

Arable weeds,cover crops,and tillage drive soil microbial community composition in organic cropping systems

Cover crops have traditionally been used to reduce soil erosion and build soil quality, but more recently cover crops are being used as an effective tool in organic weed management. Many studies have demonstrated microbial community response to individual cover crop species, but the effects of mixed species cover crop communities have received less attention. Moreover, the relationship between arable weeds and soil microbial communities is not well understood. The objective of this study was to determine the relative influence of cover crop diversity, early-season weed communities, and tillage on soil microbial community structure in an organic cropping system through the extraction of fatty acid methyl esters (FAMEs). A field experiment was conducted between 2009 and 2011 near Mead, NE where spring-sown mixtures of zero (control), two, and eight cover crop species were included in a sunflower–soybean–corn crop rotation. A mixture of four weed species was planted in all experimental units (excluding the no-cover control), and also included as an individual treatment. Cover crops and weeds were planted in late-March, then terminated in late-May using a field disk or sweep plow undercutter, and main crops were planted within one week of termination. Three (2009) or four (2010–11) soil cores were taken to a depth of 20 cm in all experimental units at 45, 32, and 25 days following cover crop termination in 2009, 2010, and 2011, respectively. Total FAMEs pooled across 2009 and 2010 were greatest in the two species mixture–undercutter treatment combination (140.8 ± 3.9 nmol g⁻¹) followed by the eight species mixture–undercutter treatment combination (132.4 ± 3.9 nmol g⁻¹). Abundance of five (2009 and 2010) and seventeen (2011) FAME biomarkers was reduced in the weedy treatment relative to both cover-cropped treatments and the no-cover control. In 2009 and 2010, termination with the undercutter reduced abundance of most actinomycete biomarkers while termination with the field disk reduced abundance of C18:1(cis11) and iC16:0. Canonical discriminant analysis of the microbial community successfully segregated most cover crop mixture by termination method treatment combinations in 2009 and 2010. Microbial communities were most strongly influenced by the presence and type of early-spring plant communities, as weeds exerted a strong negative influence on abundance of many key microbial biomarkers, including the AMF markers C16:1(cis11) and C18:1(cis11). Weeds may alter soil microbial community structure as a means of increasing competitive success in arable soils, but this relationship requires further investigation.     

Effects of cropping and tree density on earthworm community composition and densities in central Cameroon

Earthworms can have positive effects upon crop growth in the tropics. If soils are to be managed sustainably, then more attention should be paid to the effects of cultivation and cropping practices upon earthworms. When forest vegetation is cleared, slashed, burned and land is tilled and cultivated, earthworm abundance, diversity and activity are reduced. Conversely, retaining trees in agroecosystems may maintain earthworm populations during the cropping phase.Here, we assessed the impact on earthworm species diversity and densities of crop cultivation in the understorey of timber plantations thinned to two tree densities and compared these with uncropped, undisturbed timber plantation controls. The plots were reassessed after two and a half years of fallow to see whether populations had recovered. The experiment was in central Cameroon.Seventeen earthworm species were recorded from Eudrilidae subfamilies Eudrilinae and Pareudrilinae, Ocnerodrilidae and Acanthodrilidae, most of which were endemics. This included two new species from two new genera from the sub-family Pareudrilinae, one new species from one new genus of Ocnerodrilidae, two new species of Dichogaster and one new species of Legonodrilus. Ten species were epigeic, six were endogeic and one was anecic.Generally, earthworm densities were lower in cropped plots than in the undisturbed plantation control. The most abundant species was a Legonodrilus sp. nov. with average densities of 49 individuals m⁻² in the crop phase and 80 ind. m⁻² in the fallow phase. By the fallow phase, densities in the low tree density (120 ind. m⁻²) were higher than in the high density (40 ind. m⁻²). The densities of the epigeic Acanthodrilidae were significantly reduced to 7 ind. m⁻² in the cropped plots compared with 42 ind. m⁻² in the control plots. The effects of cropping were thus species-specific and more work is required to identify which of these endemics are the ecosystem engineers in the system.