Assessment of fungi in soils of sugarcane crops and their potential for production of biomass-degrading enzymes

Soil management practices are konwn to affect the biomass and enzyme activities of microbial soil communities. To assess whether burning of sugarcane prior to harvesting affects the community of soilborne fungi, we collected soil simples in two sites: burned sugarcane culture prior harvesting (BS) and non-burned sugarcane culture (NBS). A total of 75 filamentous fungal isolates were recovered from soils in both sites. Trichoderma was the most prevalent genus in both sites, followed by Fusarium, Cunninghamella and Aspergillus. The Sorensen's index (0.60) suggested a slight difference in fungi associated with both areas, with high number of fungal isolates found on BB soil. The abundance of Trichoderma isolates in NBS soil was higher than BS soil; however, the abundance of Fusarium, Aspergillus and Cunninghamella was higher in the latter type of soil. In addition, fungi isolated from BS soil showed the highest production of xylanase and laccase in comparision with fungi isolated form NBS soil. Our results indicate that the different types of sugarcane harvesting apparently did not interfere with the diversity of fungal communnities as revealed by culture-dependent methods. In addition, our data indicates the potencial of fungi from soils of sugarcane crops to produce relevant enzymes related to biomass conversion.

Bacterial communities and biogeochemical transformations of iron and sulfur in a high saltmarsh soil profile

Microbial community structure in saltmarsh soils is stratified by depth and availability of electron acceptors for respiration. However, the majority of the microbial species that are involved in the biogeochemical transformations of iron (Fe) and sulfur (S) in such environments are not known. Here we examined the structure of bacterial communities in a high saltmarsh soil profile and discuss their potential relationship with the geochemistry of Fe and S. Our data showed that the soil horizons Ag (oxic-suboxic), Bg (suboxic), Cri (anoxic with low concentration of pyrite Fe) and Cr-2 (anoxic with high concentrations of pyrite Fe) have distinct geochemical and microbiological characteristics. In general, total S concentration increased with depth and was correlated with the presence of pyrite Fe. Soluble + exchangable-Fe, pyrite Fe and acid volatile sulfide Fe concentrations also increased with depth, whereas ascorbate extractable-Fe concentrations decreased. The occurrence of reduced forms of Fe in the horizon Ag and oxidized Fe in horizon Cr-2 suggests that the typical redox zonation, common to several marine sediments, does not occur in the saltmarsh soil profile studied. Overall, the bacterial community structure in the horizon Ag and Cr-2 shared low levels of similarity, as compared to their adjacent horizons, Bg and Cr-1, respectively. The phylogenetic analyses of bacterial 16S rRNA gene sequences from clone libraries showed that the predominant phylotypes in horizon Ag were related to Alphaproteobacteria and Bacteroidetes. In contrast, the most abundant phylotypes in horizon Cr-2 were related to Deltaproteo-bacteria, Chloroflexi, Deferribacteres and Nitrospira. The high frequency of sequences with low levels of similarity to known bacterial species in horizons Ag and Cr-2 indicates that the bacterial communities in both horizons are dominated by novel bacterial species. (c) 2008 Elsevier Ltd. All rights reserved.

Soil fungal communities of grasslands are environmentally structured at a regional scale in the Alps.

Studying patterns of species distributions along elevation gradients is frequently used to identify the primary factors that determine the distribution, diversity and assembly of species. However, despite their crucial role in ecosystem functioning, our understanding of the distribution of below-ground fungi is still limited, calling for more comprehensive studies of fungal biogeography along environmental gradients at various scales (from regional to global). Here, we investigated the richness of taxa of soil fungi and their phylogenetic diversity across a wide range of grassland types along a 2800 m elevation gradient at a large number of sites (213), stratified across a region of the Western Swiss Alps (700 km(2)). We used 454 pyrosequencing to obtain fungal sequences that were clustered into operational taxonomic units (OTUs). The OTU diversity-area relationship revealed uneven distribution of fungal taxa across the study area (i.e. not all taxa are everywhere) and fine-scale spatial clustering. Fungal richness and phylogenetic diversity were found to be higher in lower temperatures and higher moisture conditions. Climatic and soil characteristics as well as plant community composition were related to OTU alpha, beta and phylogenetic diversity, with distinct fungal lineages suggesting distinct ecological tolerances. Soil fungi, thus, show lineage-specific biogeographic patterns, even at a regional scale, and follow environmental determinism, mediated by interactions with plants.

Arbuscular mycorrhizal fungal communities and soil aggregation as affected by cultivation of various crops during the sugarcane fallow period

Management systems involving crop rotation, ground cover species and reduced soil tillage can improve the soil physical and biological properties and reduce degradation. The primary purpose of this study was to assess the effect of various crops grown during the sugarcane fallow period on the production of glomalin and arbuscular mycorrhizal fungi in two Latosols, as well as their influence on soil aggregation. The experiment was conducted on an eutroferric Red Latosol with high-clay texture (680 g clay kg-1) and an acric Red Latosol with clayey texture (440 g kg-1 clay) in Jaboticabal (São Paulo State, Brazil). A randomized block design involving five blocks and four crops [soybean (S), soybean/fallow/soybean (SFS), soybean/millet/soybean (SMS) and soybean/sunn hemp/soybean (SHS)] was used to this end. Soil samples for analysis were collected in June 2011. No significant differences in total glomalin production were detected between the soils after the different crops. However, total external mycelium length was greater in the soils under SMS and SHS. Also, there were differences in easily extractable glomalin, total glomalin and aggregate stability, which were all greater in the eutroferric Red Latosol than in the acric Red Latosol. None of the cover crops planted in the fallow period of sugarcane improved aggregate stability in either Latosol.

Diversity and structure of AMF communities as affected by tillage in a temperate soil.

Arbuscular mycorrhizal fungi (AMF) were studied in differently tilled soils from a long-term field experiment in Switzerland. Diversity and structure of AMF communities were surveyed either directly on spores isolated from the field soil or on spores isolated from trap cultures, planted with different host plants. Single-spore cultures were established from the AMF spores obtained from trap cultures. Identification of the AMF was made by observation of spore morphology and confirmed by sequencing of ITS rDNA. At least 17 recognised AMF species were identified in samples from field and/or trap cultures, belonging to five genera of AMF--Glomus, Gigaspora, Scutellospora, Acaulospora, and Entrophospora. Tillage had a significant influence on the sporulation of some species and non- Glomus AMF tended to be more abundant in the no-tilled soil. The community structure of AMF in the field soil was significantly affected by tillage treatment. However, no significant differences in AMF diversity were detected among different soil tillage treatments. AMF community composition in trap cultures was affected much more by the species of the trap plant than by the original tillage treatment of the field soil. The use of trap cultures for fungal diversity estimation in comparison with direct observation of field samples is discussed.

Soil oribatid mite in four typical vegetation communities of Misiones forest in the Iguazú area, Argentina

The objective of this work was to assess the soil oribatid mite communities in four sites of the Upper Paraná Bosque Atlántico, in the Iguazú National Park, Argentina and in surrounding areas: bamboo forest, palm forest and two mixed forests. A comparison between each pair of sites, based on the presence-absence of oribatid species, was performed using Jaccard's index. This is the first systematic sampling of oribatid mites in this area. A total of 56 genera and 96 oribatid species were found, 25 and 49 of them, respectively, are new citation for Argentina. The highest similarity was found between mixed forests. Almost 68% and 34% of the genera were cited for similar biotopes in Brazil and Paraguay, respectively.

Soil-Transmitted Helminth Infections, Nutrition and Growth in School-age Children from Rural Communities in Honduras

Background: Soil-transmitted helminth (STH) infections are endemic in Honduras but their impact on children’s health is not well studied. Objectives: To evaluate the prevalence and intensity of STH infections and their association with nutrition and growth in a sample of Honduran children. Methodology: A cross-sectional study was done among Honduran rural school-age children in 2011. Blood and stool samples and anthropometric measurements were obtained to determine nutritional status, STH infection and growth status, respectively. Results: The STH prevalence among 320 studied children was 72.5%. Prevalence by species was 30%, 67% and 16% for Ascaris, Trichuris and 16% hookworms, respectively. High intensity infections were associated with decreased growth scores but regardless of intensity, co-infections negatively affected growth indicators. Conclusions: The health burden of STH infections is related to high parasitic load but also to the presence of low-intensity concurrent infections. The synergistic effects of polyparasitism in underprivileged children warrants more attention.

Risk Factors for Soil-transmitted Helminth Infections in Schoolchildren from Rural Communities in Honduras

Background: Honduras is endemic for soil-transmitted helminth (STH) infections. However, knowledge gaps remain in terms of risk factors involved in STH transmission and infection intensity. Objectives: To determine the prevalence and intensity of STH infections in schoolchildren living in rural Honduras. Additionally, to investigate risk factors associated with STH infections. Methods: A cross-sectional study was done among Honduran rural schoolchildren, in 2011. Demographic and epidemiological data were obtained and STH infections were determined using Kato-Katz method. Results: A total of 320 children completed the study. Overall and specific prevalences for Ascaris lumbricoides, Trichuris trichiura and hookworms were 72.5%, 30%, 67% and 16%, respectively. Several risk factors associated with STH transmission and infection intensity were identified at the individual and familial level as well as at the schools. Conclusions: Improving hygienic conditions and providing semi-annual deworming treatment are feasible interventions that could enhance undergoing STH control activities.

Soil-Transmitted Helminth Infections and Nutritional Status in School-age Children from Rural Communities in Honduras

Background: Soil-transmitted helminth (STH) infections are endemic in Honduras and efforts are underway to decrease their transmission. However, current evidence is lacking in regards to their prevalence, intensity and their impact on children’s health. Objectives: To evaluate the prevalence and intensity of STH infections and their association with nutritional status in a sample of Honduran children. Methodology: A cross-sectional study was done among school-age children residing in rural communities in Honduras, in 2011. Demographic data was obtained, hemoglobin and protein concentrations were determined in blood samples and STH infections investigated in single-stool samples by Kato-Katz. Anthropometric measurements were taken to calculate heightfor- age (HAZ), BMI-for-age (BAZ) and weight-for-age (WAZ) to determine stunting, thinness and underweight, respectively. Results: Among 320 children studied (48% girls, aged 7–14 years, mean 9.7661.4) an overall STH prevalence of 72.5% was found. Children .10 years of age were generally more infected than 7–10 year-olds (p = 0.015). Prevalence was 30%, 67% and 16% for Ascaris, Trichuris and hookworms, respectively. Moderate-to-heavy infections as well as polyparasitism were common among the infected children (36% and 44%, respectively). Polyparasitism was four times more likely to occur in children attending schools with absent or annual deworming schedules than in pupils attending schools deworming twice a year (p,0.001). Stunting was observed in 5.6% of children and it was associated with increasing age. Also, 2.2% of studied children were thin, 1.3% underweight and 2.2% had anemia. Moderate-to-heavy infections and polyparasitism were significantly associated with decreased values in WAZ and marginally associated with decreased values in HAZ. Conclusions: STH infections remain a public health concern in Honduras and despite current efforts were highly prevalent in the studied community. The role of multiparasite STH infections in undermining children’s nutritional status warrants more research.

Soil-Transmitted Helminths, Poverty, and Malnutrition in Honduran Children Living in Remote Rural Communities

Soil-transmitted helminth (STH) infections are endemic in Honduras, but their prevalence according to the levels of poverty in the population has not been examined. The present cross-sectional study is aimed to determine the role of different levels of poverty in STH prevalence and infection intensity as well as the potential associations of STH infections with malnutrition and anemia. Research participants were children attending a medical brigade serving remote communities in Northern Honduras in June 2014. Demographic data were obtained, and poverty levels were determined using the unsatisfied basic needs method. STH infections were investigated by the Kato-Katz method; hemoglobin concentrations were determined with the HemoCue system; and stunting, thinness, and underweight were determined by anthropometry. Data were analyzed using descriptive statistics and univariate and multivariable logistic regression models. Among 130 children who participated in this study, a high prevalence (69.2%) of parasitism was found and the poorest children were significantly more infected than those living in less poor communities (79.6% vs. 61.8%; P = 0.030). Prevalence rates of Trichuris trichiura, Ascaris lumbricoides, and hookworms were 69.2%, 12.3%, and 3.85%, respectively. In total, 69% of children had anemia and 30% were stunted. Households’ earthen floor and lack of latrines were associated with infection. Greater efforts should be made to reduce STH prevalence and improve overall childhood health, in particular, among the poorest children lacking the basic necessities of life.

Molecular biodiversity of microbial communities in polluted soils and their role in soil phytoremediation

Les métaux lourds (ML) s’accumulent de plus en plus dans les sols à l’échelle mondiale, d’une part à cause des engrais minéraux et divers produits chimiques utilisés en agriculture intensive, et d’autre part à cause des activités industrielles. Toutes ces activités génèrent des déchets toxiques qui s’accumulent dans l’environnement. Les ML ne sont pas biodégradables et leur accumulation cause donc des problèmes de toxicité des sols et affecte la biodiversité des microorganismes qui y vivent. La fertilisation en azote (N) est une pratique courante en agriculture à grande échelle qui permet d’augmenter la fertilité des sols et la productivité des cultures. Cependant, son utilisation à long terme cause plusieurs effets néfastes pour l'environnement. Par exemple, elle augmente la quantité des ML dans les sols, les nappes phréatiques et les plantes. En outre, ces effets néfastes réduisent et changent considérablement la biodiversité des écosystèmes terrestres. La structure des communautés des champignons mycorhiziens à arbuscules (CMA) a été étudiée dans des sols contaminés par des ML issus de la fertilisation à long terme en N. Le rôle des différentes espèces de CMA dans l'absorption et la séquestration des ML a été aussi investigué. Dans une première expérience, la structure des communautés de CMA a été analysée à partir d’échantillons de sols de sites contaminés par des ML et de sites témoins non-contaminés. Nous avons constaté que la diversité des CMA indigènes a été plus faible dans les sols et les racines des plantes récoltées à partir de sites contaminés par rapport aux sites noncontaminés. Nous avons également constaté que la structure de la communauté d'AMF a été modifiée par la présence des ML dans les sols. Certains ribotypes des CMA ont été plus souvent associés aux sites contaminés, alors que d’autres ribotypes ont été associés aux sites non-contaminés. Cependant, certains ribotypes ont été observés aussi bien dans les sols pollués que non-pollués. Dans une deuxième expérience, les effets de la fertilisation organique et minérale (N) sur les différentes structures des communautés des CMA ont été étudiés. La variation de la structure de la communauté de CMA colonisant les racines a été analysée en fonction du type de fertilisation. Certains ribotypes de CMA étaient associés à la fertilisation organique et d'autres à la fertilisation minérale. En revanche, la fertilisation minérale a réduit le nombre de ribotypes de CMA alors que la fertilisation organique l’a augmenté. Dans cette expérience, j’ai démontré que le changement de structure des communautés de CMA colonisant des racines a eu un effet significatif sur la productivité des plantes. Dans une troisième expérience, le rôle de deux espèces de CMA (Glomus irregulare et G. mosseae) dans l'absorption du cadmium (Cd) par des plants de tournesol cultivés dans des sols amendés avec trois niveaux différents de Cd a été évalué. J’ai démontré que les deux espèces de CMA affectent différemment l’absorption ou la séquestration de ce ML par les plants de tournesol. Cette expérience a permis de mieux comprendre le rôle potentiel des CMA dans l'absorption des ML selon la concentration de cadmium dans le sol et les espèces de CMA. Mes recherches de doctorat démontrent donc que la fertilisation en N affecte la structure des communautés des CMA dans les racines et le sol. Le changement de structure de la communauté de CMA colonisant les racines affecte de manière significative la productivité des plantes. J’ai aussi démontré que, sous nos conditions expériemntales, l’espèce de CMA G. irregulare a été observée dans tous les sites (pollués et non-pollués), tandis que le G. mosseae n’a été observé en abondance que dans les sites contaminés. Par conséquent, j’ai étudié le rôle de ces deux espèces (G. irregulare et G. mosseae) dans l'absorption du Cd par le tournesol cultivé dans des sols amendés avec trois différents niveaux de Cd en serre. Les résultats indiquent que les espèces de CMA ont un potentiel différent pour atténuer la toxicité des ML dans les plantes hôtes, selon le niveau de concentration en Cd. En conclusion, mes travaux suggèrent que le G. irregulare est une espèce potentiellement importante pour la phytoextration du Cd, alors que le G. mosseae pourrait être une espèce appropriée pour phytostabilisation du Cd et du Zn.

Evaluating the efficiency of sampling methods in assessing soil macrofauna communities in arable systems

The soil fauna is often a neglected group in many large-scale studies of farmland biodiversity due to difficulties in extracting organisms efficiently from the soil. This study assesses the relative efficiency of the simple and cheap sampling method of handsorting against Berlese-Tullgren funnel and Winkler apparatus extraction. Soil cores were taken from grassy arable field margins and wheat fields in Cambridgeshire, UK, and the efficiencies of the three methods in assessing the abundances and species densities of soil macroinver-tebrates were compared. Handsorting in most cases was as efficient at extracting the majority of the soil macrofauna as the Berlese-Tullgren funnel and Winkler bag methods, although it underestimated the species densities of the woodlice and adult beetles. There were no obvious biases among the three methods for the particular vegetation types sampled and no significant differences in the size distributions of the earthworms and beetles. Proportionally fewer damaged earthworms were recorded in larger (25 x 25 cm) soil cores when compared with smaller ones (15 x 15 cm). Handsorting has many benefits, including targeted extraction, minimum disturbance to the habitat and shorter sampling periods and may be the most appropriate method for studies of farmland biodiversity when a high number of soil cores need to be sampled. (C) 2008 Elsevier Masson SAS. All rights reserved.

Abiotic drivers and plant traits explain landscape-scale patterns in soil microbial communities

The controls on aboveground community composition and diversity have been extensively studied, but our understanding of the drivers of belowground microbial communities is relatively lacking, despite their importance for ecosystem functioning. In this study, we fitted statistical models to explain landscape-scale variation in soil microbial community composition using data from 180 sites covering a broad range of grassland types, soil and climatic conditions in England. We found that variation in soil microbial communities was explained by abiotic factors like climate, pH and soil properties. Biotic factors, namely community- weighted means (CWM) of plant functional traits, also explained variation in soil microbial communities. In particular, more bacterial-dominated microbial communities were associated with exploitative plant traits versus fungal-dominated communities with resource-conservative traits, showing that plant functional traits and soil microbial communities are closely related at the landscape scale.