Diversity and infectivity of arbuscular mycorrhizal fungi in agricultural soils of the Sichuan Province of mainland China

Knowledge about the presence and diversity of arbuscular mycorrhizal fungi (AMF) in a specific area is an essential first step for utilizing these fungi in any application. The community composition of AMF in intensively managed agricultural soil in the Sichuan Province of southwest China currently is unknown. In one set of samples, AMF were trapped in pot cultures from 40 fields growing legumes in the Panxi region, southeast Sichuan. In a second set of samples, the MPN method with four-fold dilutions and maize as host was used to estimate infective propagules in soil from another 50 agricultural sites throughout the province. Soil types were heterogeneous and were classified as purple, yellow, paddy and red. Crops at each site were either maize, wheat or sweet orange. From this set of soil, AMF spores were also extracted and identified. Including all ninety soils, thirty glomeromycotan species in Glomus (20 species), Acaulospora (four species), Scutellospora (three species), Ambispora (one species), Archaeospora (one species) and Paraglomus (one species) were identified. Yellow, red and purple soils yielded similar numbers of AMF species, while AMF species diversity was clearly lower in paddy soil. In trap culture soils, the most frequent species were Glomus aggregatum or Glomus intraradices, Glomus claroideum and Glomus etunicatum. The species Acaulospora capsicula, Acaulospora delicata, G. aggregatum (or intraradices), G. claroideum, Glomus epigaeum, G. etunicatum, Glomus luteum, Glomus monosporum, Glomus mosseae and Glomus proliferum were successfully cultured as single-species pot cultures in Plantago lanceolata. The three most frequent species in field soils were G. mosseae, Glomus caledonium and Glomus constrictum. MPN values varied between 17 and 3334 propagules 100 g soil⁻¹ among the fifty field sites sampled. Regression analysis, including host&soil, log(P) and pH as explanatory variables explained 59% of the variation in log(MPN). The highest MPN estimates were found in purple soil cropped with maize and citrus, 324 and 278 propagules 100 g soil⁻¹, respectively. The lowest MPN value, 54 propagules 100 g soil⁻¹, was measured in wheat in purple and yellow soil. Despite intensive agricultural management that can include often repeated tillage, our examination of 90 agricultural sites revealed that soils of the Sichuan region have moderate to high numbers of infective AMF propagules as well as a high AMF species diversity. This opens possibilities for further studies and utilization of AMF in agriculture and horticulture in the Sichuan province, People’s Republic of China.     

Biodegradation of pentachorophenol by tropical basidiomycetes in soils contaminated with industrial residues

Summary The ability of tropical Brazilian basidiomycetes to degrade pentachlorophenol (PCP) in soils from areas contaminated with organochlorine industrial residues was studied. Thirty-six basidiomycetes isolated from different tropical ecosystems were tested for tolerance to high PCP concentrations in soil. Peniophoracinereaand Psilocybecastanella, two strains of Trametes villosa,Agrocybe perfecta, Trichaptum bisogenumand Lentinus villosuswere able to colonize soil columns containing up to 4600 mg pentachlorophenol kg⁻¹soil. The first four species were inoculated into soil containing 1278 mg pentachlorophenol kg⁻¹ soil supplemented with gypsum and sugar cane bagasse. P. cinerea,P.castanella, T. villosaCCB176 and CCB213 and Agrocybe perfectareduced the PCP present in the contaminated soil by 78, 64, 58, 36 and 43%, respectively, after 90 days of incubation. All fungi mineralized [¹⁴C] pentachlorophenol, mainlyP. cinereaandT. villosawith the production of 7.11 and 8.15% ¹⁴CO₂, respectively, during 120 days of incubation. All fungi produced chloride ions during growth on soil containing PCP, indicating dehalogenation of the molecule. Conversion of PCP to pentachloroanisole was observed only after 90 days of incubation in soils inoculated with A. perfecta, P.cinereaand one of T. villosastrain. The present study shows the potential of Brazilian fungi for the biodegradation of toxic and persistent pollutants and it is the first to report fungal growth and PCP depletion in soils with high pentachlorophenol concentrations.     

Nitric oxide production in agricultural soils

Numerous papers on nitric oxide have been published covering various aspects ranging from its solution and gas-phase chemistry, biochemical and physiological functions and atmospheric processes. This review emphasizes recent developments in the literature relating to NO/NOx production in agricultural soils. We have tried to minimize overlap with other recent and relevant review articles. Emission measurements that have been made since 1992 are tabulated and discussed in terms of variability, fertilization effects, and advances made in monitoring fluxes. We describe attempts made by a number of authors to utilize ecological markers such as aeration, water, ammonium, nitrate content, etc. in order to distinguish between nitrification and denitrification as the primary source of production and/or consumption in natural field situations. This may allow a rational accounting for the high spatial and temporal variability observed, and the formulation of reliable predictive models. Factors such as diffusion, oxygen, water, and carbon (content and quality) that regulate or significantly influence production, consumption and emission are discussed. Finally some important implications of recent research relating to nitrification and denitrification is presented showing the chemical oxidation of NO which could occur when the acetylene inhibition technique is used.     

Wood-inhabiting ligninolytic basidiomycetes in soils: Ecology and constraints for applicability in bioremediation

Ligninolytic basidiomycetes associated with wood decay are a physiologically distinct group of saprotrophic fungi capable of decomposition of all major components of wood. Although wood is their natural substrate, several species can survive in soil if suitable substrates are available, the soil-colonizing ability of species in the genera Phanerochaete, Pleurotus and Trametes being comparable to that of the soil-inhabiting basidiomycetes utilizing plant litter. Wood-inhabiting ligninolytic basidiomycetes (WLB) in soil interact with soil microflora, and some species are very efficient competitors affecting both the soil microbial biomass and the composition of the indigenous microbial community. The extracellular enzymes utilized by saprotrophic basidiomycetes for nutrient acquisition participate in the interspecific interactions with other soil biota but are also involved in the transformation of soil organic matter – lignocellulose and humic compounds. Bioremediation research has significantly enriched our knowledge of the ecology of basidiomycetes, but it has also identified several limitations for practical applicability of WLB at a field scale, and has led to the conclusion that natural attenuation or bioaugmentation are todays methods of choice for on site treatment.     

Diversity of saproxylic basidiomycetes in Quercus ilex woodlands of central and insular Greece

The sclerophyllous forests of Quercus ilex (holm oak) possess a unique position in earth’s biosphere, existing only in countries of the Mediterranean basin. However, very little information exists about mushrooms associated with holm oak in east Mediterranean, including Greece, where Q. ilex appears mostly in relict forests and fragmented stands. A pertinent long-term investigation was undertaken in selected Q. ilex dominated habitats of Crete, Andros, Naxos and Ikaria islands (Aegean Archipelago) as well as in mountains of Attica. Specimens of xylotrophic basidiomycetes were collected and identified. As a result, 74 species were recorded; among them Hemimycena cephalotricha, Hyphoderma cremeoalbum, Hyphodontia radula, Irpex litschaueri, Mycena algeriensis, Phanerochaete martelliana, Phloeomana alba and Phlebia unica constitute new records for the Greek mycobiota, while 68 species are reported for the first time on Q. ilex in Greece. Moreover, the presence of Fomitiporia mediterranea on this host was evidenced through ITS sequencing, and comments are made about its relationship to F. punctata and F. pseudopunctata. The importance of findings is discussed in conjunction with their environmental value; five species could be assigned in the “Species of Special Interest” categories, and other five polypores are proposed as suitable indicators for Q. ilex habitat assessment and conservation.     

Diversity of Archaea in Brazilian savanna soils

Although the richness of Bacteria and Fungi in Cerrado’ soils has been reported, here we report, for the first time, the archaeal community in Cerrado’s soils. DNA extracted from soil of two distinct vegetation types, a dense subtype of sensu strict (cerrado denso) and riverbank forest (mata de galeria), was used to amplify Archaea-specific 16S rRNA gene. All of the fragments sequenced were classified as Archaea into the phylum Thaumarchaeota, predominantly affiliated to groups I.1b and I.1c. Sequences affiliated to the group I.1a were found only in the soil from riverbank forest. Soils from ‘cerrado denso’ had greater Archaea richness than those from ‘mata de galeria’ based on the richness indexes and on the rarefaction curve. β-Diversity analysis showed significant differences between the sequences from the two soil areas studied because of their different thaumarchaeal group composition. These results provide information about the third domain of life from Cerrado soils.     

Evaluation of carbon accrual in afforested agricultural soils

Afforestation of agricultural lands can provide economically and environmentally realistic C storage to mitigate for elevated CO₂ until other actions such as reduced fossil fuel use can be taken. Soil carbon sequestration following afforestation of agricultural land ranges from losses to substantial annual gains. The present understanding of the controlling factors is inadequate for understanding ecosystem dynamics, modeling global change and for policy decision‐makers. Our study found that planting agricultural soils to deciduous forests resulted in ecosystem C accumulations of 2.4 Mg C ha⁻¹ yr⁻¹ and soil accumulations of 0.35 Mg C ha⁻¹ yr⁻¹. Planting to conifers showed an average ecosystem sequestration of 2.5 and 0.26 Mg C ha⁻¹ yr⁻¹ in the soils but showed greater field to field variability than when planted to deciduous forest. Path analysis showed that Ca was positively related to soil C accumulations for both conifers and deciduous afforested sites and played a significant role in soil C accumulations in these sites. Soil N increases were closely related to C accumulation and were two times greater than could be explained by system N inputs from atmospheric deposition and natural sources. Our results suggest that the addition of Ca to afforested sites, especially conifers, may be an economical means to enhance soil C sequestration even if it does not result in increasing C in aboveground pools. The mechanism of N accumulation in these aggrading stands needs further investigation.     

Diversity of mesophilic clostridia in Costa Rican soils

Costa Rica is located in the Tropic, one of the most biologically diverse regions of the world; its soil is an important epicenter of biodiversity and Clostridium spp. are among the most frequent bacteria. The diversity of clostridia in Costa Rican soils and its possible association with geographic zone, pH or type of soil was studied in 117 soil samples: 18 from the Atlantic Zone, 30 from the Central Plateau, 30 from the Dry Pacific, 13 from the North Zone, and 26 from the South Pacific. The pH and the mesophilic clostridia species were determined for each sample. For bacterial isolation, a selective methodology for spores and pre-reduced anaerobically sterilized media were used. A total of 1945 strains of clostridia were isolated, 98% were identified and corresponded to 54 species; the most frequent species were C. subterminale (56%), C. oceanicum (51%), C. bifermentans and C. glycolicum (50%, each), C. sporogenes (49%), and C. sordellii (42%). An average of 7.1 species per sample was obtained; the Atlantic Zone showed the greatest diversity: 8.6 species per sample and a total of 45 species. Except for C. chauvoei, all described toxigenic clostridia species were isolated; C. sordellii (42%) and C. perfringens (38%) were the most frequent. No statistical relation could be established between geographic zone or type of soil and any species, showing that clostridia had a high adaptation capability to grow in different soil conditions; only some clostridia were isolated from very acidic samples while others from soils with a wide range of pH. In general, a uniform distribution of most species and a high variety of clostridia in Costa Rican soils were observed, in agreement with the high biodiversity described for other living beings in this country.     

Diversity of frankiae in soils from five continents

Clone libraries of nifH gene fragments specific for the nitrogen-fixing actinomycete Frankia were generated from six soils obtained from five continents using a nested PCR. Comparative sequence analyses of all libraries (n=247 clones) using 96 to 97% similarity thresholds revealed the presence of three and four clusters of frankiae representing the Elaeagnus and the Alnus host infection groups, respectively. Diversity of frankiae was represented by fewer clusters (i.e., up to four in total) within individual libraries, with one cluster generally harboring the vast majority of sequences. Meta-analysis including sequences previously published for cultures (n=48) and for uncultured frankiae in root nodules of Morella pensylvanica formed in bioassays with the respective soils (n=121) revealed a higher overall diversity with four and six clusters of frankiae representing the Elaeagnus and the Alnus host infection groups, respectively, and displayed large differences in cluster assignments between sequences retrieved from clone libraries and those obtained from nodules, with assignments to the same cluster only rarely encountered for individual soils. These results demonstrate large differences between detectable Frankia populations in soil and those in root nodules indicating the inadequacy of bioassays for the analysis of frankiae in soil and the role of plants in the selection of frankiae from soil for root nodule formation.     

Bacterial diversity in agricultural soils during litter decomposition

Denaturing gradient gel electrophoresis (DGGE) of amplified fragments of genes coding for 16S rRNA was used to study the development of bacterial communities during decomposition of crop residues in agricultural soils. Ten strains were tested, and eight of these strains produced a single band. Furthermore, a mixture of strains yielded distinguishable bands. Thus, DGGE DNA band patterns were used to estimate bacterial diversity. A field experiment performed with litter in nylon bags was used to evaluate the bacterial diversity during the decomposition of readily degradable rye and more refractory wheat material in comparable luvisols and cambisols in northern, central, and southern Germany. The amount of bacterial DNA in the fresh litter was small. The DNA content increased rapidly after the litter was added to the soil, particularly in the rapidly decomposing rye material. Concurrently, diversity indices, such as the Shannon-Weaver index, evenness, and equitability, which were calculated from the number and relative abundance (intensity) of the bacterial DNA bands amplified from genes coding for 16S rRNA, increased during the course of decomposition. This general trend was not significant for evenness and equitability at any time. The indices were higher for the more degradation-resistant wheat straw than for the more easily decomposed rye grass. Thus, the DNA band patterns indicated that there was increasing bacterial diversity as decomposition proceeded and substrate quality decreased. The bacterial diversity differed for the sites in northern, central, and southern Germany, where the same litter material was buried in the soil. This shows that in addition to litter type climate, vegetation, and indigenous microbes in the surrounding soil affected the development of the bacterial communities in the litter.     

Patterns of metabolites produced from the fluoroquinolone enrofloxacin by basidiomycetes indigenous to agricultural sites

Supernatants of mycelial cultures of seven basidiomycetous fungi indigenous to agricultural sites were evaluated for metabolites generated from the veterinary fluoroquinolone enrofloxacin (EFL) by employing high–performance liquid chromatography/high–resolution electrospray ionization mass spectrometry. From exact masses, molecular formulae were derived, and the most probable chemical structures were deduced. Patterns of major metabolites were surprisingly similar but differed greatly from that provided by Gloeophyllum striatum due to the absence of monohydroxylated EFL congeners and a greater variety of metabolites with a modified piperazine moiety. The structures of three metabolites were elucidated by ¹H–nuclear magnetic resonance spectroscopy. Of 61 compounds detected, 48 were new, while 13 were known from a pattern of 87 EFL metabolites identified for G. striatum. Ethylpiperazine moieties carrying oxido, hydroxy, oxo, and acetoxy groups, or showing partial degradation, were linked to the unmodified, oxidatively decarboxylated, or multiply hydroxylated core of EFL and to isatin– and anthranilic acid–type EFL congeners. Cleavage of the fluoro–aromatic bond was observed for two, ¹⁴CO₂ formation for six species. Metabolites with a hydroxylated aromatic part implied subsequent ring cleavage to be brought about by the formation of potentially four oxidizable ortho–aminophenol– and one catechol–type intermediates. EFL degradation appears to be a common activity among basidiomycetes.     

Diversity of green-like and red-like ribulose-1,5-bisphosphate carboxylase/oxygenase large-subunit genes (cbbL) in differently managed agricultural soils

A PCR-based approach was developed to detect ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) form I large-subunit genes (cbbL) as a functional marker of autotrophic bacteria that fix carbon dioxide via the Calvin-Benson-Bassham cycle. We constructed two different primer sets, targeting the green-like and red-like phylogenetic groups of cbbL genes. The diversity of these cbbL genes was analyzed by the use of three differently managed agricultural soils from a long-term field experiment. cbbL gene fragments were amplified from extracted soil DNAs, and PCR products were cloned and screened by restriction fragment length polymorphism analysis. Selected unique cbbL clones were sequenced and analyzed phylogenetically. The green-like cbbL sequences revealed a very low level of diversity, being closely related to the cbbL genes of Nitrobacter winogradskyi and Nitrobacter vulgaris. In contrast, the red-like cbbL gene libraries revealed a high level of diversity in the two fertilized soils and less diversity in unfertilized soil. The majority of environmental red-like cbbL genes were only distantly related to already known cbbL sequences and even formed separate clusters. In order to extend the database of available red-like cbbL sequences, we amplified cbbL sequences from bacterial type culture strains and from bacterial isolates obtained from the investigated soils. Bacterial isolates harboring the cbbL gene were analyzed phylogenetically on the basis of their 16S rRNA gene sequences. These analyses revealed that bacterial genera such as Bacillus, Streptomyces, and Arthrobacter harbor red-like cbbL genes which fall into the cbbL gene clusters retrieved from the investigated soils.     

Diversity of facultatively anaerobic microscopic mycelial fungi in soils

The numbers of microscopic fungi isolated from soil samples after anaerobic incubation varied from tens to several hundreds of CFU per one gram of soil; a total of 30 species was found. This group is composed primarily of mitotic fungi of the ascomycete affinity belonging to the orders Hypocreales (Fusarium solani, F. oxysporum, Fusarium sp., Clonostachys grammicospora, C. rosea. Acremonium sp., Gliocladium penicilloides, Trichoderma aureoviride, T. harzianum, T. polysporum, T. viride. T. koningii, Lecanicillum lecanii, and Tolypocladium inflatum) and Eurotiales (Aspergillus terreus, A. niger, and Paecilomyces lilacimus), as well as to the phylum Zygomycota, to the order Mucorales (Actinomucor elegans, Absidia glauca, Mucor circinelloides, M. hiemalis, M. racemosus, Mucor sp., Rhizopus oryzae, Zygorrhynchus moelleri, Z. heterogamus, and Umbelopsis isabellina) and the order Mortierellales (Mortierella sp.). As much as 10-30% of the total amount of fungal mycelium remains viable for a long time (one month) under anaerobic conditions.     

Plasmid incidence in bacteria from agricultural and industrial soils

Heavy metal contents of agricultural and industrial soils were determined by atomic absorption spectrophotometry. The analysis of the samples collected from two different locations revealed significantly high levels of Fe, Zn, Cu, Cr and Ni. Certain microbiological parameters (total aerobic heterotrophs, asymbiotic N₂-fixers, total Actinomycetes and fungi) were also monitored from these soils. A total of 70 bacterial isolates from agricultural and industrial soils were examined for plasmid DNA content and resistance to the antibiotics amoxycillin, cloxacillin, chloramphenicol, doxycycline methicillin, nalidixic acid, and tetracycline. Minimum inhibitory concentrations (MICs) of Cu, Cr, Pb, Cd, Hg, Zn, and Ni for each isolate were also determined. Resistance was most frequent to methicillin (48.5%), cloxacillin (45.7%), and nalidixic acid (40%) for all isolates of bacteria. The highest MICs observed were 100 g/ml for mercury, 800 g/ml for Ni and 1600 g/ml for other metals. The incidences of metal resistance and MICs of metals for bacteria from industrial soil were significantly different to those of agricultural soil. On a percentage basis, 91.4% of the total bacterial isolates from industrial soil were found to harbour plasmids whereas 40% of the isolates from agricultural soil contained plasmids.     

Diversity and ecology of wood-inhabiting aphyllophoroid basidiomycetes on fallen woody debris in various forest types in Switzerland

This study on the ecology of aphyllophoroid wood-inhabiting basidiomycetes in Switzerland showed a remarkably high species diversity of both saprophytes and mycorrhiza-forming species. Phlebiella vaga, a saprophytic species, and Amphinema byssoides, a mycorrhizal symbiont, were the two most abundant species. A total of 3339 samples of fungal fruitbodies in 86 plots distributed all over Switzerland belonged to 238 species. The five main biogeographical regions of Switzerland showed different pattern of fungal species richness: while the Plateau at lower altitudes was found to be rather rich, the Northern Alps and Central Alps, with the highest amount of forests cover, yielded less species. Although the Southern Alps exhibited the lowest species richness, this region harbours a specific species set. These findings encourage for further studies in Central Europe, where many species of aphyllophoroid wood-inhabiting basidiomycetes seem to be highly under-investigated.     

Phylogenetic diversity of fluorescent pseudomonads in agricultural soils from Korea

AIMS: To identify and compare the relative diversity and distribution of genotypes of culturable fluorescent pseudomonads from soils. METHODS AND RESULTS: Analysis of 160 isolates from seven soil samples using randomly amplified polymorphism DNA methods revealed 53 genotypes, which were subsequently identified by their 16S ribosomal DNA sequences. Phylogenetic analyses of the 53 genotypes along with 43 fluorescent pseudomonad type strains separated the genotypes into 10 distinct clusters that included two phylogenetic groups that were not represented by previously described type strains. CONCLUSIONS: The diversity of genotypes that was obtained from the soil samples was highly variable among the different soils and appeared to be associated with different soil management practices that also influence plant yields. SIGNIFICANCE AND IMPACT OF THE STUDY: The identification and phylogenetic analysis of these genotypes offers opportunities for study of phenotypic traits that may be associated within taxonomically related groups of fluorescent pseudomonad species and how these groups vary in relation to soil management practices.     

Diversity of antifungal actinomycetes in various vegetative soils of Korea

Diversity of actinomycetes and their antifungal activities against some plant pathogenic fungi were examined in various vegetative soils from 14 different sites in the western part of Korea. Actinomycete counts ranged from 1.17 x 10(6) to 4.20 x 10(6) cfu x g(-1) dried soil. A total of 1510 actinomycetes were isolated from the soil samples. Streptomyces was predominant in soils with a pH range of 5.1-6.5, 9.1-13.0% moisture, and 9.1-11.0% organic matter. Most Micromonospora, Dactylosporangium, and Streptosporangium were distributed in soils with pH 4.0-5.0, 2.0-9.0% moisture, and 4.0-7.0% organic matter. Actinomadura and nocardioform actinomycetes were abundant in soils with pH 4.0-5.0 and 13.1-20.0% moisture and with 9.1-11.0 and 4.0-7.0% organic matter, respectively. Populations of Streptomyces were predominant in all the soils, but were highest in grassland and lowest in mountain-forest soils. Micromonospora was most abundant in pepper-field soil and nocardioform actinomycetes were highest in rice paddy field soil. Dactylosporangium was predominant in lake-mud sediments and pepper-field soil, Streptosporangium in lake-mud sediments, and Actinomadura in mountain-forest soil. Antifungal actinomycetes were abundant in orchard soil and lake mud. More than 50% of antifungal isolates from most soils were classified as genus Streptomyces. Actinomycete isolates that showed strong antifungal activity against Alternaria mali, Colletotrichum gloeosporioides, Fusarium oxysporum f.sp. cucumerinum, and Rhizoctonia solani were predominant in pepper-field soils, whereas those against Magnaporthe grisea and Phytophthora capsici were abundant in radish-field soils.     

New directions for improving the management of agricultural soils

Idowu et al., in this edition of Plant and Soil describe a welcome new tool that allows farmers to optimize the management of their fields. It is based on a holistic approach that integrates assays of soil physical, chemical and biological parameters into an easily understandable, low-cost and quantitative estimate of soil quality or “health”. It can facilitate tracking and understanding of the short and long term effects of different management approaches on soil (and crop) health. Most of the assays used are based on traditional, labour-intensive techniques. The tool could be improved through employment of assay technologies that are under development. For example, Idowu et al., in this edition investigated the use of near infra-red spectroscopy as a replacement for some of the traditional soil assays. Similarly, future developments in remote spectroscopic assays, using satellite, airborne or land-based platforms may facilitate further improvement.