Organic farming promotes the abundance of fungi keystone taxa in bacteria-fungi interkingdom networks.

Soil bacteria-fungi interactions are essential in the biogeochemical cycles of several nutrients, making these microbes major players in agroecosystems. While the impact of the farming system on microbial community composition has been extensively reported in the literature, whether sustainable farming approaches can promote associations between bacteria and fungi is still unclear. To study this, we employed 16S, ITS, and 18S DNA sequencing to uncover how microbial interactions were affected by conventional and organic farming systems on maize crops. The Bray-Curtis index revealed that bacterial, fungal, and arbuscular mycorrhizal fungi communities were significantly different between the two farming systems. Several taxa known to thrive in healthy soils, such as Nitrosophaerales, Orbiliales, and Glomus were more abundant in the organic farming system. Constrained ordination revealed that the organic farming system microbial community was significantly correlated with the ß-glucosidase activity, whereas the conventional farming system microbial community significantly correlated with soil pH. Both conventional and organic co-occurrence interkingdom networks exhibited a parallel node count, however, the former had a higher number of edges, thus being denser than the latter. Despite the similar amount of fungal nodes in the co-occurrence networks, the organic farming system co-occurrence network exhibited more than 3-fold the proportion of fungal taxa as keystone nodes than the conventional co-occurrence network. The genera Bionectria, Cercophora, Geastrum, Penicillium, Preussia, Metarhizium, Myceliophthora, and Rhizophlyctis were among the fungal keystone nodes of the organic farming system network. Altogether, our results uncover that beyond differences in microbial community composition between the two farming systems, fungal keystone nodes are far more relevant in the organic farming system, thus suggesting that bacteria-fungi interactions are more frequent in organic farming systems, promoting a more functional microbial community.

Can arbuscular mycorrhizal fungi and rhizobacteria facilitate 33P uptake in maize plants under water stress?

Arbuscular mycorrhizal fungi (AMF) and plant growth-promoting rhizobacteria (PGPR) are able to provide key ecosystem services, protecting plants against biotic and abiotic stresses. Here, we hypothesized that a combination of AMF (Rhizophagus clarus) and PGPR (Bacillus sp.) could enhance 33P uptake in maize plants under soil water stress. A microcosm experiment using mesh exclusion and a radiolabeled phosphorus tracer (33P) was installed using three types of inoculation: i) only AMF, ii) only PGPR, and iii) a consortium of AMF and PGPR, alongside a control treatment without inoculation. For all treatments, a gradient of three water-holding capacities (WHC) was considered i) 30% (severe drought), ii) 50% (moderate drought), and iii) 80% (optimal condition, no water stress). In severe drought conditions, AMF root colonization of dual-inoculated plants was significantly lower compared to individual inoculation of the AMF, whilst 33P uptake by dual-inoculated plants or plants inoculated with bacteria was 2.4-fold greater than the uninoculated treatment. Under moderate drought conditions the use of AMF promoted the highest 33P uptake by plants, increasing it by 2.1-fold, when compared to the uninoculated treatment. Without drought stress, AMF showed the lowest 33P uptake and, overall, plant P acquisition was lower for all inoculation types when compared to the severe and moderate drought treatments. The total shoot P content was modulated by the water-holding capacity and inoculation type, with the lowest values observed under severe drought and the highest values under moderate drought. The highest soil electrical conductivity (EC) values were found under severe drought in AMF-inoculated plants and the lowest EC for no drought in single or dual-inoculated plants. Furthermore, water-holding capacity influenced the total soil bacterial and mycorrhizal abundance over time, with the highest abundances being found under severe and moderate drought. This study demonstrates that the positive influence of microbial inoculation on 33P uptake by plants varied with soil water gradient. Furthermore, under severe stress conditions, AMF invested more in the production of hyphae, vesicles and spore production, indicating a significant carbon drain from the host plant as evidenced by the lack of translation of increased 33P uptake into biomass. Therefore, under severe drought the use of bacteria or dual-inoculation seems to be more effective than individual AMF inoculation in terms of 33P uptake by plants, while under moderate drought, the use of AMF stood out.

Microbiome Associated with Olive Cultivation: A Review.

International research has devoted much effort to the study of the impacts caused to the soil by different management practices applied to olive cultivation. Such management involves techniques considered conventional, including the control of spontaneous plants with herbicides or machines, inorganic fertilizers, and pesticides to control pests and diseases. Equally, some producers use sustainable techniques, including drastic pruning, the use of cultivars that are tolerant to diseases and adverse climates, the use of organic conditioners in the soil, the maintenance of vegetation cover with spontaneous plants, and the use of inoculants, among others. In both conventional and sustainable/organic management, the effects on soil quality, crop development, and production are accessed through the presence, activity, and/or behavior of microorganisms, microbial groups, and their processes in the soil and/or directly in the crop itself, such as endophytes and epiphytes. Thus, our present review seeks to assemble research information, not only regarding the role of microorganisms on growth and development of the olive tree (Olea europaea L.). We looked mainly for reviews that reveal the impacts of different management practices applied in countries that produce olive oil and olives, which can serve as a basis and inspiration for Brazilian studies on the subject.

Organic farming practices change the soil bacteria community, improving soil quality and maize crop yields.

BACKGROUND: The importance of organic farming has increased through the years to promote food security allied with minimal harm to the ecosystem. Besides the environmental benefits, a recurring problem associated with organic management is the unsatisfactory yield. A possible solution may rely on the soil microbiome, which presents a crucial role in the soil system. Here, we aimed to evaluate the soil bacterial community structure and composition under organic and conventional farming, considering the tropical climate and tropical soil. METHODOLOGY: Our organic management treatments were composed by composted poultry manure and green manure with Bokashi. Both organic treatments were based on low nitrogen inputs. We evaluated the soil bacterial community composition by high-throughput sequencing of 16S rRNA genes, soil fertility, and soil enzyme activity in two organic farming systems, one conventional and the last transitional from conventional to organic. RESULTS: We observed that both organic systems evaluated in this study, have higher yield than the conventional treatment, even in a year with drought conditions. These yield results are highly correlated with changes in soil chemical properties and enzymatic activity. The attributes pH, Ca, P, alkaline phosphatase, and ß- glucosidase activity are positively correlated with organic systems, while K and Al are correlated with conventional treatment. Also, our results show in the organic systems the changes in the soil bacteria community, being phyla Acidobacteria, Firmicutes, Nitrospirae, and Rokubacteria the most abundant. These phyla were correlated with soil biochemical changes in the organic systems, helping to increase crop yields. CONCLUSION: Different organic management systems, (the so-called natural and organic management systems, which use distinct organic sources), shift the soil bacterial community composition, implying changes in their functionalities. Also, our results contributed to the identification of target bacterial groups and changes in soil chemical properties and enzymatic activity in a trophic organic farming system, which may contribute to higher crop yields.

Nitrogen-fixing trees in mixed forest systems regulate the ecology of fungal community and phosphorus cycling.

The fungal community plays an important role in forest ecosystems via the provision of resources to plant nutrition and productivity. However, the ecology of the fungal network and its relationship with phosphorus (P) dynamics remain poorly understood in mixed forest plantations. Here, we analyzed the fungal community using the amplicon sequencing in plantations of pure Eucalyptus grandis, with (E + N) and without N fertilization (E), besides pure Acacia mangium (A), and in a consortium of E. grandis and A. mangium (E + A), at 27 and 39 months after planting. We analyzed chemical, physical and biochemical soil and litter attributes related to P cycling, and the fungal community structure to find out if mixed plantations can increase fungal connections and to identify their role in the P dynamics in the soil-litter system. Soil organic fraction (OF), phosphorus in OF, total-P and acid phosphatase activity were significantly higher in E + A and A treatments regardless of the sampling period. Total N and P, richness, and Shannon diversity of the fungi in the litter was significantly higher in the treatments E + A and A. The fungal community structure in litter differed between treatments and sampling periods, and E + A showed an intermediate structure between the two pure treatments (E) and (A). E + A correlated highly with P dynamics when evaluated by both Pearson and redundancy analyses, particularly in the litter layer. Co-occurrence networks of fungal taxa became simpler in pure E. grandis plantations, whereas mixed system (E + A) showed a more connected and complex network. Our findings provide novel evidence that mixed forest plantations promote positive responses in the fungal community connections, which are closely related to P availability in the system, prominently in the litter layer. This indicates that the litter layer represents a specific niche to improve nutrient cycling by fungi in mixed forest ecosystems.

Ecotoxicological effects of swine manure on Folsomia candida in subtropical soils.

The production model used in Brazilian pig farms promotes a concentration of animals in small territorial extensions, causing difficulty in disposing of the manure generated, since the economically viable alternative is to use this as an agricultural fertilizer. The objective was to evaluate the effect of swine manure doses on the biological and behavioral parameters in Folsomia candida by ecotoxicological tests. An Ultisol, Oxisol and Tropical Artificial Soil (TAS) were contaminated with 0, 25, 50, 75 and 100 m3 ha-1 of swine manure, to which springtails were exposed for evaluation of mortality, and the doses 0, 10, 15, 20 and 25 m3 ha-1 of swine manure to evaluated reproduction and avoidance. Lethality was observed in all doses as well as all soils, indicating toxicity of the manure. In the reproduction tests dose since 10 m3 ha-1 caused a reduction of juveniles in all soils. Avoidance behavior was observed in all doses of the Oxisol treatments and at 20 and 25 m3 ha-1 in Ultisol treatments. However, in TAS occurred not avoidance response of F. candida. We conclude that the swine manure was toxic to F. candida and the toxicity is dependent on the soil characteristics and the manure concentrations applied.

Acacia Changes Microbial Indicators and Increases C and N in Soil Organic Fractions in Intercropped Eucalyptus Plantations.

Intercropping forest plantations of Eucalyptus with nitrogen-fixing trees can increase soil N inputs and stimulate soil organic matter (OM) cycling. However, microbial indicators and their correlation in specific fractions of soil OM are unclear in the tropical sandy soils. Here, we examined the microbial indicators associated with C and N in the soil resulting from pure and intercropped Eucalyptus grandis and Acacia mangium plantations. We hypothesized that introduction of A. mangium in a Eucalyptus plantation promotes changes in microbial indicators and increases C and N concentrations on labile fractions of the soil OM, when compared to pure eucalyptus plantations. We determined the microbial and enzymatic activity, and the potential for C degradation by the soil microbial community. Additionally, we evaluated soil OM fractions and litter parameters. Soil (0-20 cm) and litter samples were collected at 27 and 39 months after planting from the following treatments: pure E. grandis (E) and A. mangium (A) plantations, pure E. grandis plantations with N fertilizer (E+N) and an E. grandis, and A. mangium intercropped plantations (E+A). The results showed that intercropped plantations (E+A) increase 3, 45, and 70% microbial biomass C as compared to A, E+N, and E, at 27 months after planting. The metabolic quotient (qCO2) showed a tendency toward stressful values in pure E. grandis plantations and a strong correlation with dehydrogenase activity. A and E+A treatments also exhibited the highest organic fractions (OF) and C and N contents. A canonical redundancy analysis revealed positive correlations between microbial indicators of soil and litter attributes, and a strong effect of C and N variables in differentiating A and E+A from E and E+N treatments. The results suggested that a significant role of A. mangium enhance the dynamics of soil microbial indicators which help in the accumulation of C and N in soil OF in intercropped E. grandis plantations. Our results are mostly relevant to plantations in sandy soil areas with low levels of OM, suggesting and efficient method for improving nutrient availability in the soil and optimizing eucalyptus growth and development.

Effect of phosphate-solubilizing bacteria on phosphorus dynamics and the bacterial community during composting of sugarcane industry waste.

Sugarcane processing generates a large quantity of residues, such as filter cake and ashes, which are sometimes composted prior to their amendment in soil. However, important issues still have to be addressed on this subject, such as the description of bacterial succession that occurs throughout the composting process and the possibilities of using phosphate-solubilizing bacteria (PSB) during the process to improve phosphorus (P) availability in the compost end product. Consequently, this study evaluated the bacterial diversity and P dynamics during the composting process when inoculated with Pseudomonas aeruginosa PSBR12 and Bacillus sp. BACBR01. To characterize the bacterial community structure during composting, and to compare PSB-inoculated compost with non-inoculated compost, partial sequencing of the bacterial 16S rRNA gene and sequential P fractionation were used. The data indicated that members of the order Lactobacillales prevailed in the early stages of composting for up to 30 days, mostly due to initial changes in pH and the C/N ratio. This dominant bacterial group was then slowly replaced by Bacillales during a composting process of up to 60 days. In addition, inoculation of PSB reduced the levels of Ca-bound P by 21% and increased the labile organic P fraction. In PSB-inoculated compost, Ca-P compound solubilization occurred concomitantly with an increase of the genus Bacillus. The bacterial succession and the final community is described in compost from sugarcane residues and the possible use of these inoculants to improve P availability in the final compost is validated.

Ecotoxicological characterization of sugarcane vinasses when applied to tropical soils.

The impact of sugarcane vinasse on soil invertebrates was assessed through ecotoxicological assays. Increasing concentrations of two vinasses from different distillery plants (VA and VB), and a vinasse from a laboratory production (VC), were amended on two natural tropical Oxisols (LV and LVA) and a tropical artificial soil (TAS) to characterize the effects of the vinasses on earthworms (Eisenia andrei), enchytraeids (Enchytraeus crypticus), mites (Hypoaspis aculeifer) and collembolans (Folsomia candida). The highest concentrations of VA and VB were avoided by earthworms in all soils and by collembolans especially in the natural soils. The presence of VC in all of the tested soils did not cause avoidance behavior in these species. The reproduction of earthworms, enchytraeids and collembolans was decreased in the highest concentrations of VA and VB in the natural soils. In TAS, VB reduced the reproduction of all test species, whereas VA was toxic exclusively to E. andrei and E. crypticus. The vinasse VC only reduced the number of earthworms in TAS and enchytraeids in LVA. The reproduction of mites was reduced by VB in TAS. Vinasses from distillery plants were more toxic than the vinasse produced in laboratory. The vinasse toxicities were influenced by soil type, although this result was most likely because of the way the organisms are exposed to the contaminants in the soils. Toxicity was attributed to the vinasses' high salt content and especially the high potassium concentrations. Data obtained in this study highlights the potential risk of vinasse disposal on tropical soils to soil biota. The toxic values estimated are even more relevant when considering the usual continuous use of vinasses in crop productions.

Bacterial community characterization in the soils of native and restored rainforest fragments.

The Brazilian Atlantic Forest ("Mata Atlântica") has been largely studied due to its valuable and unique biodiversity. Unfortunately, this priceless ecosystem has been widely deforested and only 10 % of its original area is still untouched. Some projects have been successfully implemented to restore its fauna and flora but there is a lack of information on how the soil bacterial communities respond to this process. Thus, our aim was to evaluate the influence of soil attributes and seasonality on soil bacterial communities of rainforest fragments under restoration processes. Soil samples from a native site and two ongoing restoration fragments with different times of implementation (10 and 20 years) were collected and assayed by using culture-independent approaches. Our findings demonstrate that seasonality barely altered the bacterial distribution whereas soil chemical attributes and plant species were related to bacterial community structure during the restoration process. Moreover, the strict relationship observed for two bacterial groups, Solibacteriaceae and Verrucomicrobia, increasing from the more recently planted (10 years) to the native site, with the 20 year old restoration site in the middle, which may suggest their use as bioindicators of soil quality and recovery of forest fragments being restored.

Seed dressing pesticides on springtails in two ecotoxicological laboratory tests.

Terrestrial ecotoxicological tests are powerful tools for assessing the ecological risks that pesticides pose to soil invertebrates, but they are rarely used to evaluate seed dressing pesticides. This study investigated the effects of seed dressing pesticides on survival and reproduction of Folsomia candida (Collembola), using standardized ecotoxicological tests (after ISO guidelines with few adaptations for tropical conditions). Commercial formulations of five seed dressing pesticides were tested individually in Tropical Artificial Soil (TAS): the insecticides imidacloprid, fipronil, thiametoxam, and the fungicides captan and carboxin+thiram. Thiametoxam, captan, and carboxin+thiram were only lethal to F. candida at the highest concentration tested (1000mg of active ingredient kg(-1) of dry soil). Imidacloprid and fipronil were lethal at lower concentrations (100 and 10mg a.i. kg(-1) soil d.w, respectively), however, these concentrations were much higher than those predicted (PEC) for soil. Imidacloprid and fipronil were the most toxic pesticides in both tests, reducing significantly collembolan reproduction (EC20=0.02 and 0.12mga.i.kg(-1) soil d.w, respectively). Further studies under more realistic conditions are needed, since imidacloprid and fipronil reduced collembolan reproduction at concentrations below or close to their respective PECs.

Diversity and symbiotic effectiveness of beta-rhizobia isolated from sub-tropical legumes of a Brazilian Araucaria Forest.

While the occurrence of Betaproteobacteria occupying the nodules of tropical legumes has been shown, little is known about subtropical areas. Araucaria Forest is a subtropical endangered ecosystem, and a better understanding of the legume-rhizobial symbionts may allow their use in land reclamation. The 16S rRNA gene of bacteria isolated from nine leguminous species was sequenced and their nodulation tested in Mimosa scabrella and Phaseolus vulgaris. 196 isolates were identified as eight genotypes: Pantoea, Pseudomonas, Bradyrhizobium sp1-2, Rhizobium, and Burkholderia sp1-3. The majority of the isolates from native plants (87 %) were taxonomically related to ß-rhizobia, namely Burkholderia, however the legumes Galactia crassifolia and Collea speciosa were nodulated by both α and ß-rhizobia, and Acacia dealbata, an exotic plant, only by α-rhizobia. The nifH genes of some isolates were sequenced and N-fixing potential shown by the acetylene reduction test. Most of the isolates nodulated the test plants, some were effective in M. scabrella, but all presented low efficiency in the exotic promiscuous legume P. vulgaris. Pantoea and Pseudomonas did not nodulate and probably are endophytic bacteria. The presented data shows diversity of α, ß and γ-Proteobacteria in nodules of subtropical legumes, and suggests host specificity with ß-rhizobia. Potential isolates were found for M. scabrella, indicating that a high N-fixing strain may be further inoculated in plants for use in reforestation.

Earthworm ecotoxicological assessments of pesticides used to treat seeds under tropical conditions.

Ecotoxicological laboratory tests (lower-tier tests) are fundamental tools for assessing the toxicity of pesticides to soil organisms. In this study, using these tests under tropical conditions, we quantified the impact of the insecticides imidacloprid, fipronil, and thiametoxam, and the fungicides captan and carboxin+thiram, all of which are used in the chemical treatment of crop seeds, on the survival, reproduction, and behavior of Eisenia andrei (Oligochaeta). With the exception of imidacloprid, none of the pesticides tested caused mortality in E. andrei in artificial soils. The LC(50) of imidacloprid was estimated as 25.53 mg active ingredient kg(-1) of dry soil. Earthworm reproduction rates were reduced by imidacloprid (EC(50)=4.07 mgkg(-1)), fipronil (EC(20)=23.16 mgkg(-1)), carboxin+thiram (EC(50)=56.38 mgkg(-1)), captan (EC(50)=334.84 mgkg(-1)), and thiametoxam (EC(50)=791.99 mgkg(-1)). Avoidance behavior was observed in the presence of imidacloprid (AC(50)=0.11 mgkg(-1)), captan (AC(50)=33.54 mgkg(-1)), carboxin+thiram (AC(50)=60.32 mgkg(-1)), and thiametoxam (AC(50)=>20 mgkg(-1)). Earthworms showed a preference for soils with the insecticide fipronil. Imidacloprid was the most toxic of the substances tested for E. andrei. The avoidance test was the most sensitive test for most pesticides studied, but results varied between pesticides. These results offer new insights on the toxicity of pesticides used to treat seeds in tropical regions. However, they should be complemented with higher-tier tests in order to reduce the uncertainties in risk assessment.

Dosage-dependent shift in the spore community of arbuscular mycorrhizal fungi following application of tannery sludge.

The controlled disposal of tannery sludge in agricultural soils is a viable alternative for recycling such waste; however, the impact of this practice on the arbuscular mycorrhizal fungi (AMF) communities is not well understood. We studied the effects of low-chromium tannery sludge amendment in soils on AMF spore density, species richness and diversity, and root colonization levels. Sludge was applied at four doses to an agricultural field in Rolândia, Paraná state, Brazil. The sludge was left undisturbed on the soil surface and then the area was harrowed and planted with corn. The soil was sampled at four intervals and corn roots once within a year (2007/2008). AMF spore density was low (1 to 49 spores per 50 cm(3) of soil) and decreased as doses of tannery sludge increased. AMF root colonization was high (64%) and unaffected by tannery sludge. Eighteen AMF species belonging to six genera (Acaulospora, Glomus, Gigaspora, Scutellospora, Paraglomus, and Ambispora) were recorded. At the sludge doses of 9.0 and 22.6 Mg ha(-1), we observed a decrease in AMF species richness and diversity, and changes in their relative frequencies. Hierarchical grouping analysis showed that adding tannery waste to the soil altered AMF spore community in relation to the control, modifying the mycorrhizal status of soil and selectively favoring the sporulation of certain species.

Sporulation and diversity of arbuscular mycorrhizal fungi in Brazil Pine in the field and in the greenhouse.

The aim of this work was to assess the sporulation and diversity of arbuscular mycorrhizal fungi (AMF) at different forest sites with Araucaria angustifolia (Bert.) O. Ktze. (Brazil Pine). In addition, a greenhouse experiment was carried out to test the use of traditional trap plants (maize + peanut) or A. angustifolia to estimate the diversity of AMF at each site. Soil samples were taken in two State Parks at southwestern Brazil: Campos do Jordão (Parque Estadual de Campos do Jordão [PECJ]) and Apiaí (Parque Estadual Turístico do Alto Ribeira [PETAR]), São Paulo State, in sites of either native or replanted forest. In PECJ, an extra site of replanted forest that was impacted by accidental fire and is now in a state of recuperation was also sampled. The spore densities and their morphological identification were compiled at each site. In the greenhouse, soil samples from each site were used as inoculum to promote spore multiplication on maize + peanut or A. angustifolia grown on a sandy, low-fertility substrate. Plants were harvested, respectively, after 4 months or 1 year of growth and assessed for mycorrhizal root colonization. Spore counts and identification were also performed in the substrate, after the harvest of plants. Twenty-five taxa were identified considering all sites. Species richness and diversity were greater in native forest areas, being Acaulospora, the genus with the most species. Differences in number of spores, diversity, and richness were found at the different sites of each State Park. Differences were also found when maize + peanut or A. angustifolia were used as trap plants. The traditional methodology using trap plants seems to underestimate the diversity of the AMF. The use of A. angustifolia as trap plant showed similar species richness to the field in PECJ, but the identified species were not necessarily the same. Nevertheless, for PETAR, both A. angustifolia and maize + peanut underestimated the species richness. Because the AMF sporulation can be affected by many conditions, it is impossible to draw detailed conclusions from this kind of survey. More precise experiments have to be set up to isolate the different factors that modulate the ecophysiological interactions between host plant and endophyte.

Arbuscular mycorrhizal fungi associated with Araucaria angustifolia (Bert.) O. Ktze.

Specimens of Araucaria angustifolia from a native forest reserve and a reforested area in the State Park of Campos do Jordão were studied to determine the number and diversity of spore populations of arbuscular mycorrhizal fungi (AMF) and root colonization. Six randomly chosen plots (planted with 8- to 12-year-old plants) were delimited, four in the native forest and two in the reforested area. Rhizosphere and root samples were collected during two periods of the year corresponding to the rainy and dry seasons. A greenhouse experiment was set up for multiplication of field propagules (from the native forest and reforested area) for two consecutive generations. Araucaria leaves from the experimental plots were collected during the first sampling for nutrient analysis. Twenty-four AMF taxa were found and percent AM colonization was determined in all plots. Not all AMF species observed in the field were re-isolated through the recovery pot cultures, even after a second cultivation cycle. The foliar nutrient analysis showed higher nutrient levels in plants from the native forest than the reforested area. Generally, spore richness and diversity were highest during the warmer and more humid period and in the native forest plants.