Primary Decomposers Research Articles

Dynamic succession of microbial compost communities and functions during Pleurotus ostreatus mushroom cropping on a short composting substrate.

Cultivating oyster mushrooms (Pleurotus ostreatus), a typical primary decomposer of lignocellulose, on a short composting substrate is a novel procedure which possesses energy conserves, reduced the chance of infection by competitive species, shorter production duration and achieved high production efficiency. However, the microbiome and microbial metabolic functions in the composting substrate during the mushroom cropping is unknown. In the present study, the contents of hemicellulose, cellulose and lignin and the activities of protease, laccase and cellulase were evaluated in the corncob short composting substrate from before oyster mushroom spawning to first flush fructification; meanwhile the changes in the microbiome and microbial metabolic functions were surveyed by using metagenomic sequencing. Results showed that the hemicellulose, cellulose and lignin in the short composting substrate were decomposed of 42.76, 34.01, and 30.18%, respectively, during the oyster mushroom cropping process. In addition, the contents of hemicellulose, cellulose and lignin in the composting substrate were reduced rapidly and negatively correlated with the abundance of the Actinobacteria phylum. The activities of protease, laccase and cellulase fastly increased in the period of before oyster mushroom spawning to full colonization and were positively correlated to the abundance of Actinobacteria phylum. The total abundance of bacteria domain gradually decreased by only approximately 15%, while the abundance of Actinobacteria phylum increased by 68% and was positively correlated with that of oyster mushroom. The abundance of oyster mushroom increased by 50 times from spawning to first flush fructification. The dominant genera, all in the order of Actinomycetales, were Cellulosimicrobium, Mycobacterium, Streptomyces and Saccharomonospora. The total abundance of genes with functions annotated in the Clusters of Orthologous Groups of proteins (COG) for Bacteria and Archaea and Kyoto Encyclopedia of Genes and Genomes (KEGG) database for all three life domains was positively correlated. The three metabolic pathways for carbohydrates, amino acids and energy were the primary enrichment pathways in KEGG pathway, accounting for more than 30% of all pathways, during the mushroom cropping in which the glycine metabolic pathway, carbon fixation pathways in prokaryotes and methane metabolism were all dominated by bacteria. The genes of cellulolytic enzymes, hemicellulolytic enzymes, laccase, chitinolytic enzymes, peptidoglycanlytic enzymes and ammonia assimilation enzymes with abundances from 0.28 to 0.24%, 0.05 to 0.02%, 0.02 to 0.01%, 0.14 to 0.08%, 0.39 to 0.16%, and 0.13 to 0.12% during the mushroom cropping identified in the Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups (eggNOG) database for all three life domains were all aligned to COG database. These results indicated that bacteria, especially Actinomycetales, were the main metabolism participants in the short composting substrate during the oyster mushroom cropping. The relationship between oyster mushrooms and bacteria was cooperative, Actinomycetales were oyster mushroom growth promoting bacteria (OMGPB).

Analysis on the growth of fungal population and the interaction between population

The carbon cycle is an important part of the geochemical cycle of the Earth. As the primary decomposers of organic material in terrestrial ecosystems, fungi are critical agents of the global carbon cycle. Based on the two characteristics of a fungus, the growth rate of the fungus and the fungus’ tolerance to moisture, this article will establish a mathematical model to describe fungi and their role in the decomposition of ground litter (dead plant material) and woody fibers. First of all, the growth rate of a single fungus population was determined by modifying the Logistic population growth model. According to the hyphal extension rate of a fungus comprehensively measured by temperature and humidity changes, the effect of hyphal extension rate on wood decomposition rate is obtained. Next, this article uses the competitive ranking of fungi and the moisture niche width to determine the moisture tolerance of fungi and the influence of fungus moisture tolerance on wood decomposition rate. Integrating the hyphal extension rate and moisture tolerance of fungi, we established a wood decomposition rate model for a single fungus community. Based on this model and Lotka-Volterra model, this paper quantified and described the interaction between different types of fungi, and constructed a model of wood decomposition rate under the interaction of multiple fungal populations. Finally, the sensitivity and stability of the model are analyzed and tested. For the role and importance of biodiversity in the ecosystem, we conducted a more comprehensive study, and analyzed the role and principle of biodiversity in the process of environmental factors change.

Trophic structure and origin of resources of soil macrofauna in the salt marsh of the Wadden Sea: a stable isotope (15N, 13C) study

Salt marshes exist along the gradient of the marine mudflat to the terrestrial dunes, with a gradient of shore height and associated plant zonation. The lower salt marsh (LSM) extends from the mean high tidal level to 35 cm above that level and is followed by the upper salt marsh (USM). Despite changes in the amount of allochthonous marine input and in abiotic conditions, little is known about changes in the trophic structure and used of basal resources by the soil macrofauna along marine—terrestrial boundaries. Natural variations in carbon stable isotope ratios (δ13C signatures) allow insight into basal resources of consumers such as marine algae, terrestrial C3 and C4 photosynthesising plants. Furthermore, variations in nitrogen stable isotope ratios (δ15N signatures) allow insight into the trophic position of consumers. We investigated spatial and temporal changes in stable isotope signatures in salt marsh soil macrofauna of the island of Spiekeroog, German Wadden Sea. The range of δ15N signatures indicated no changes in food chain length across salt marsh zones with consumers in both zones comprising primary decomposers, secondary decomposers and first order predators. However, the trophic position of individual species changed between zones, but in particular with season. Contrasting δ15N signatures, the range in δ13C signatures in the LSM was twice that in the USM indicating a wider range of resources consumed. Bayesian mixing models indicated predominant autochthonous resource use in both the LSM and USM, with the use of marine allochthonous resources never exceeding 29.6%. However, the models also indicate an increase in the use of marine resources in certain species in the LSM with no use in the USM. Overall, the results indicate that the resource use of salt marsh macrofauna varies more in space than in time, with the food web being generally based on autochthonous rather than allochthonous resources. However, there also is trophic plasticity in certain species across both temporal and spatial scales including variations in the use of allochthonous resources. Generally, however, marine input contributes little to the nutrition of salt marsh soil macroinvertebrates.

Habitat Significantly Affect CWD Decomposition but No Home-Field Advantage of the Decomposition Found in a Subtropical Forest, China

The home-field advantage (HFA) effect has been reported to occur in coarse woody debris (CWD) and litter. It is thought that the HFA effect may be due to the specialization of decomposers in their original habitats. However, the relative contribution of microorganisms, particularly fungi and bacteria, to deadwood decomposition is unclear because of differences in their functional at-tributes and carbon requirements, and the microorganisms that drive the HFA effect of deadwood are also unclear. Here, we analysed a dataset of microbial PLFA and substrate properties collected from the soil and CWD of two subtropical trees, Cryptomeria japonica and Platycarya strobilacea, from forests dominated by one or the other of the two species, with both species present in the forests. Our results showed that habitat and tree types all significantly affected CWD respiration rates, the CWD respiration rates were significantly higher in the deciduous broadleaf forests (DBF) than in the coniferous forest (CF) regardless of tree types, but no a large HFA of CWD decomposition found (HFA index was 4.75). Most biomarkers indicated bacteria and fungi were more abundant in the DBF than in the CF, and the concentration of microbial PLFAs was higher in Platycarya strobilacea than in Cryptomeria japonica. In addition, the relative abundance of fungi and soil B/F were remarkably positively correlated with CWD respiration, indicating that fungi may be the primary decomposers of CWD. In conclusion, our work highlights the importance of interactions between the three primary drivers (environment, substrate quality and microbes) on CWD decomposition.

Original Leaf Colonisers Shape Fungal Decomposer Communities of Phragmites australis in Intermittent Habitats.

Common reed (Phragmites australis) has high biomass production and is primarily subjected to decomposition processes affected by multiple factors. To predict litter decomposition dynamics in intermittent lakes, it is critical to understand how communities of fungi, as the primary decomposers, form under different habitat conditions. This study reports the shotgun metagenomic sequencing of the initial fungal communities on common reed leaves decomposing under different environmental conditions. We demonstrate that a complex network of fungi forms already on the plant persists into the decomposition phase. Phragmites australis leaves contained at least five fungal phyla, with abundant Ascomycota (95.7%) and Basidiomycota (4.1%), identified as saprotrophs (48.6%), pathotrophs (22.5%), and symbiotrophs (12.6%). Most of the correlations between fungi in fresh and decomposing leaves were identified as co-occurrences (positive correlations). The geographic source of litter and leaf age did not affect the structure and diversity of fungal communities. Keystone taxa were mostly moisture-sensitive. Our results suggest that habitat has a strong effect on the formation of the fungal communities through keystone taxa. Nevertheless, it can also alter the proportions of individual fungal groups in the community through indirect effects on competition between the fungal taxa and their exploitation of favourable conditions.

Incorporation of mineral nitrogen into the soil food web as affected by plant community composition.

Although nitrogen (N) deposition is increasing globally, N availability still limits many organisms, such as microorganisms and mesofauna. However, little is known to which extent soil organisms rely on mineral‐derived N and whether plant community composition modifies its incorporation into soil food webs. More diverse plant communities more effectively compete with microorganisms for mineral N likely reducing the incorporation of mineral‐derived N into soil food webs. We set up a field experiment in experimental grasslands with different levels of plant species and functional group richness. We labeled soil with 15NH4 15NO3 and analyzed the incorporation of mineral‐derived 15N into soil microorganisms and mesofauna over 3 months. Mineral‐derived N incorporation decreased over time in all investigated organisms. Plant species richness and presence of legumes reduced the uptake of mineral‐derived N into microorganisms. In parallel, the incorporation of mineral‐derived 15N into mesofauna species declined with time and decreased with increasing plant species richness in the secondary decomposer springtail Ceratophysella sp. Effects of both plant species richness and functional group richness on other mesofauna species varied with time. The presence of grasses increased the 15N incorporation into Ceratophysella sp., but decreased it in the primary decomposer oribatid mite Tectocepheus velatus sarekensis. The results highlight that mineral N is quickly channeled into soil animal food webs via microorganisms irrespective of plant diversity. The amount of mineral‐derived N incorporated into soil animals, and the plant community properties affecting this incorporation, differed markedly between soil animal taxa, reflecting species‐specific use of food resources. Our results highlight that plant diversity and community composition alter the competition for N in soil and change the transfer of N across trophic levels in soil food webs, potentially leading to changes in soil animal population dynamics and community composition. Sustaining high plant diversity may buffer detrimental effects of elevated N deposition on soil biota.

Graphene environmental biodegradation: Wood degrading and saprotrophic fungi oxidize few-layer graphene

The environmental biodegradability profile of graphene related materials (GRMs) is important to know in order to predict whether these materials will accumulate in soil or will be transformed by primary decomposers. In this study, few-layer graphene (FLG) was exposed to living and devitalized axenic cultures of two white-rot basidiomycetes (Bjerkandera adusta and Phanerochaete chrysosporium) and one soil saprotrophic ascomycete (Morchella esculenta) with or without lignin, for a period of four months. Over this time, the increase of fungal biomass and presence of H2O2 and oxidizing enzymes [laccase/peroxidase and lignin peroxidase (LiP)] in growth media was assessed by gravimetric and spectrophotometric measurements, respectively. Raman spectroscopy and transmission electron microscopy (TEM) were used to compare the structure of FLG before and after incubation. All of the test fungi decreased pH in growth media and released H2O2 and laccase/peroxidase, but only basidiomycetes released LiP. Independent of growth media composition all fungi were found to be capable to oxidize FLG to a graphene oxide-like material, including M. esculenta, which released only laccase/peroxidase, i.e. the most common enzymes among primary decomposers. These findings suggest that FLG involuntarily released into terrestrial environments would likely be oxidized by soil microflora.

Macro and mesofauna soil food webs in two temperate grasslands: responses to forestation with Eucalyptus

We studied the effects of land use change from grassland to Eucalyptus spp. plantation on macro and mesofauna soil food webs in two sites in the Rolling Pampas. We expected to find differences in the parameters that characterize the structure of soil food webs, as the implantation of Eucalyptus implies changes in the characteristics of the resources and the microhabitat conditions. We also expected to find differences in the communities in terms of diversity, abundance, and species present. The treatments were: grasslands; 10-year-old Eucalyptus plantations and 20-year-old Eucalyptus plantations. Seasonal samplings were performed for the extraction of soil fauna in winter, spring, summer and autumn. For the analysis of food webs, we worked with “trophic species'': groups of organisms that have the same prey and the same predators. A total of 25 food webs were laid out using bibliographical information of feeding habits from the identified taxa. From each food web, we obtained a predator overlap graph, in which the consumers that share the same source or prey are linked by an arrow. In addition, the Shannon-Wiener index was calculated. We found that trophic species densities were different among the treatments: communities from grassland and the younger plantations were dominated by earthworms and other secondary decomposers, while the community in the older plantation showed a greater contribution of primary decomposers (Shymphyla, Isopoda and Diplopoda). No significant differences between treatments were found in the parameters that characterize the structure of soil food webs, i.e. connections number, number of trophic species nor connectivity. However, the diversity of the community was lower in the youngest plantations than in the other treatments, and it shows evidence of compartmentalization in the predator overlap graphs. Our findings suggest that the meso and macrofauna communities in the 10-years-old plantations represent a transition between the communities from grasslands and the oldest plantations. We conclude that the effects of forestation with Eucalyptus on soil fauna communities are evident through changes in functional groups rather than changes in the parameters that characterize the structure of soil food webs.

Communities of Mucorales (phylum Mucoromycota) in different ecosystems of the Atlantic Forest

ABSTRACT As primary decomposers of organic matter, mucoralean fungi have an important ecological role in edaphic systems in the Atlantic Forest. However, there is a knowledge gap regarding how communities of Mucorales are structured in soils of Atlantic Forest areas, and whether these communities are influenced by edaphic attributes in this domain. Thus, the current study aimed to understand the influence of edaphic attributes linked to species richness, abundance and composition of Mucorales in dense ombrophilous forest, ‘tabuleiro’ forest, sandbank and mangrove ecosystems located in Pernambuco, Brazil. Altogether, twenty-three taxa, including seven new records, were reported from soil samples from the ecosystems. Species composition was similar among the ecosystems, except for mangrove, while species richness and diversity of Mucorales were highest in dense ombrophilous forest and ‘tabuleiro’. Together the soil variables were responsible for 35.5 % of the variation in species composition, with pH being responsible for 53.32 % and 47.24 % of the variation in richness and abundance of these communities, respectively. These data indicate that pH is the most important attribute in delimiting the structure of mucoralean communities in the study areas, with influence on the composition, richness, and abundance of these fungi.

Eucalypt harvest residue management influences microbial community structure and soil organic matter fractions in an afforested grassland

Retaining harvest residues (HR) in the field is considered an option to recycle carbon (C) and nutrients in short-rotation plantations, but the fate of HR in the soil remains unclear. The effects of HR management and nitrogen (N) availability on soil organic matter (SOM) pools and microbial community structure of forest plantations represent a major knowledge gap. To fill this gap, we explored how management scenarios that differed in the amount and type of HR [removal of all residues (-R), residue retention without (+R/-B), or with bark (+R/+B)] and N availability [0 (-N) or 200 kg N ha-1 (+N)] influenced microbial activity and structure and SOM fractions in a recently afforested grassland. Specifically, we measured HR decomposition, carbon dioxide efflux (respired CO2), phospholipid fatty acid (PLFA), and determined changes in particulate (POM) and mineral-associated organic matter (MAOM) over 12 months using differences in δ13C natural abundance between Eucalyptus HR and grassland soils (δ13C ∼-28 ‰ and -13 ‰, respectively). Microbial respiration was stimulated by HR retention (+R). Bark retention reduced HR half-life by ∼70 days, on average, while N had little influence. Bacterial groups (Gram-positive and Gram-negative) were the primary decomposer of eucalypt HR, while Actinobacteria used more of the former soil organic carbon (SOC). +R/+B increased fungal biomarker PLFA concentration and fungal:bacterial ratio, suggesting a key role of Fungi in the fragmentation of woody HR. N influence on microbial community structure and SOM pools was dependent upon HR management. Retaining HR increased SOC concentrations, most significantly in the 0–1 cm soil depth and POM fraction, and when bark was included. +R/+B resulted in higher POM-C concentrations (up to +37%) and more depleted δ13C-POM compared with -R and +R/-B, respectively. Collectively, our results suggest it is feasible to increase POM-C and fungal abundance through HR management practices in the early stages of decomposition, which may potentially contribute to SOC stabilization in the long-term. Yet our findings remain to be tested in long-term studies, we provide quantitative evidence of the potential of a more conservative HR management to contribute to the sustainability of eucalypt plantations.

Distribution of the Termite Reproductive Castes in Gunungpati, Semarang, Central Java

Soil termites play a role as a primary decomposer in natural forests. These types of termites can be turned into residential pests as more land use to be plantations, housing, and buildings. This study analyzed the distribution of subterranean termites' reproductive caste, its identification, and environmental factors that influence the development of subterranean termites. The research methods used include distribution analysis using UV flying traps, surveys using GPS, identification of reproductive castes, and environmental factors including soil nutrients, vegetation analysis, temperature, soil moisture, air humidity, and wind speed. The results showed that the distribution of termites is found throughout the Gunungpati Semarang area. The identification of reproductive caste/alates found was Termitidae. Environmental factors that affect the life of termites in the Gunungpati Semarang area December 2019-January 2020 include the temperature of 27.0-28.4 oC, the humidity of 60.2 -61.2 %, air pressure 950.5-975.0 hPa, soil pH 4.84 - 5.60 and soil moisture 29.7-34.0 %. The vegetation was dominated by the Apocynaceae, Sapindaceae, and Euphorbiaceae. The highest value of diversity and vegetation index sequentially are Sekaran, Patemon, and Ngijo. It is found that the entire Gunungpati area of Semarang is a suitable habitat for the growth and development of the Termitidae. The finding will help the authoritative institution to consider Gunungpati as a conservation area.

Valorization of Olive Pruning Residues through Bioconversion into Edible Mushroom Pleurotus ostreatus (Jacq. Ex Fr.) P. Kumm. (1871) of Improved Nutritional Value.

In several Mediterranean countries, olive pruning residues (OLPRs) are abandoned or burned leading to several environmental problems. Valorization of these agrowastes could be a challenge for the primary decomposer Pleurotus ostreatus, turning them into edible biomass. The OLPR was used alone (OLPR), or in mixtures with wheat straw (WS : OLPR 1 : 3 v/v and WS : OLPR 3 : 1 v/v). Mycelial colonization was hastened by 3.7 days in WS : OLPR 1 : 3 (v/v). Yields were comparable to control (WS) in WS : OLPR 3 : 1 (v/v). Organic matter loss decreased with increasing proportions of OLPR in substrates. The nutritional value of mushrooms was improved by lower fat and sodium contents, in WS : OLPR 1 : 3 (v/v) and WS : OLPR 3 : 1 (v/v), and higher total protein, crude fiber, iron, and total carbohydrates contents in WS : OLPR 3 : 1 (v/v), compared with those of control. Polyunsaturated fatty acids, mainly linoleic acid, were the most abundant in mushrooms. Monounsaturated fatty acids increased in mushrooms of the substrates containing OLPR. A good predictive model of partial least square regression analysis showed different relationships of mushroom palmitic, oleic, linolenic, palmitoleic, and stearic acids with substrate composition. Findings suggested the use of OLPR as a supplement to commercial wheat straw and as a tool to reduce the negative impacts of their hazardous disposal on the environment.

A trait-based understanding of wood decomposition by fungi

As the primary decomposers of organic material in terrestrial ecosystems, fungi are critical agents of the global carbon cycle. Yet our ability to link fungal community composition to ecosystem functioning is constrained by a limited understanding of the factors accounting for different wood decomposition rates among fungi. Here we examine which traits best explain fungal decomposition ability by combining detailed trait-based assays on 34 saprotrophic fungi from across North America in the laboratory with a 5-y field study comprising 1,582 fungi isolated from 74 decomposing logs. Fungal growth rate (hyphal extension rate) was the strongest single predictor of fungal-mediated wood decomposition rate under laboratory conditions, and accounted for up to 27% of the in situ variation in decomposition in the field. At the individual level, decomposition rate was negatively correlated with moisture niche width (an indicator of drought stress tolerance) and with the production of nutrient-mineralizing extracellular enzymes. Together, these results suggest that decomposition rates strongly align with a dominance-tolerance life-history trade-off that was previously identified in these isolates, forming a spectrum from slow-growing, stress-tolerant fungi that are poor decomposers to fast-growing, highly competitive fungi with fast decomposition rates. Our study illustrates how an understanding of fungal trait variation could improve our predictive ability of the early and midstages of wood decay, to which our findings are most applicable. By mapping our results onto the biogeographic distribution of the dominance-tolerance trade-off across North America, we approximate broad-scale patterns in intrinsic fungal-mediated wood decomposition rates.

The Missing Metric: An Evaluation of Fungal Importance in Wetland Assessments

To preserve wetland ecosystem function, federal and state agencies have developed assessment procedures to better manage remaining wetland areas. Currently, wetland assessments do not consider microorganisms when determining wetland quality. This is notable, because fungi are often the primary decomposers of organic material and thus important players in nutrient cycling. The objective of this study is to quantify how wetland quality, as measured using the Ohio Rapid Assessment Method (ORAM), relates to fungal community composition. We sampled soils from six depressional emergent marshes in Ohio belonging to each of the three ORAM quality categories, assessed soil physicochemical properties, and recovered fungal DNA. We then determined if wetland quality as expressed by the ORAM reflects soil health. Our results indicate that ORAM scoring methodology significantly explains differences in fungal community composition between wetlands. We also found that soil physicochemical properties not currently included in the ORAM are strong drivers of fungal community composition, particularly bulk density, pH, soil organic matter, and soil moisture. Overall, our results suggest fungal community composition reflects wetland quality as assessed by the ORAM, and that the ORAM and potentially other wetland assessments could better capture the soil environment by including easily measured soil physicochemical properties.

Estimating population size for Macrotermes gilvus Hagen (Blattodea: Termitidae) in Indonesia

Macrotermes gilvus Hagen (Blattodea: Termitidae) is a common mound-building termite species found in South East Asia regions, particularly in Indonesia, Malaysia, Singapore, Philippines and Thailand. However, scientific information on their demography and mound construction in Indonesian natural forests had not yet reported. This study aimed to investigate the demography and mound construction of M. gilvus Hagen in Yanlappa forest, which represents low-land natural forest in West Java, Indonesia. Termites mound distribution survey was conducted in strip transect, 50 m width interval, and supported by Global Positioning System. Termites population in each mound was determined after dismantled of the mounds, meanwhile mound construction were observed vertical as well as horizontal section. The mound of M. gilvus was distributed clusterly with density of 5 mound/Ha, density mainly located at elevation 3% - 5%, and under Leaf Area Index of 0-2. We concluded that M. gilvus is primary decomposers and contribute to litter fragmentation and the recycling of nutrient into the soil. Macrotermes gilvus plays an important role as a source of heterogeneity in this ecosystem, particularly in under stresses condition. The density and dynamic of M. gilvus, be taken into account in the global strategy of the forest resources management and conservation.

Conventional and organic soil management as divergent drivers of resident and active fractions of major soil food web constituents

Conventional agricultural production systems, typified by large inputs of mineral fertilizers and pesticides, reduce soil biodiversity and may negatively affect ecosystem services such as carbon fixation, nutrient cycling and disease suppressiveness. Organic soil management is thought to contribute to a more diverse and stable soil food web, but data detailing this effect are sparse and fragmented. We set out to map both the resident (rDNA) and the active (rRNA) fractions of bacterial, fungal, protozoan and metazoan communities under various soil management regimes in two distinct soil types with barley as the main crop. Contrasts between resident and active communities explained 22%, 14%, 21% and 25% of the variance within the bacterial, fungal, protozoan, and metazoan communities. As the active fractions of organismal groups define the actual ecological functioning of soils, our findings underline the relevance of characterizing both resident and active pools. All four major organismal groups were affected by soil management (p < 0.01), and most taxa showed both an increased presence and an enlarged activity under the organic regime. Hence, a prolonged organic soil management not only impacts the primary decomposers, bacteria and fungi, but also major representatives of the next trophic level, protists and metazoa.

Organic amendment strengthens interkingdom associations in the soil and rhizosphere of barley (Hordeum vulgare)

Anthropogenic modification of soil systems has diverse impacts on food web interactions and ecosystem functioning. To understand the positive, neutral or adverse effects of agricultural practices on the associations of community members of soil microbes and microfaunal biomes, we characterized the effects of different fertilization types (organic, inorganic and a combination of organic and inorganic) on the food web active communities in the bulk soil and rhizosphere compartments in field conditions. We examined the influence of fertilization on (i) individual groups (bacteria, protozoa and fungi as microbe representatives and metazoans as microfauna representatives) and (ii) inter-kingdom interactions (focusing on the interactions between bacteria and eukaryotic groups) both neglecting and considering environmental factors in our analysis in combination with the microbial compositional data. Our results revealed different patterns of biota communities under organic versus inorganic fertilization, which shaped food web associations in both the bulk and rhizosphere compartments. Overall, organic fertilization increased the complexity of microbial–microfaunal ecological associations with inter- and intra- connections among categories of primary decomposers (bacteria and fungi) and predators (protozoa and microfauna) and differences in potential function in the soil food web in both the bulk and rhizosphere compartments. Furthermore, the inter-connections between primary decomposers and predators in bulk soil were more pronounced when environmental factors were considered. We suggest that organic fertilization selects bacterial orders with different potential ecological functions and interactions as survival, predation and cooperation due to more complex environment than those of inorganic or combined fertilization. Our findings support the importance of a comprehensive understanding of trophic food web patterns for soil management systems.

Mushrooms in Saudi Arabia (local and imported)

Mushrooms the beautiful edible macrofungi are important medicinally and nutritionally. The present study attempts to explore the locally grown mushrooms and also the imported varieties. Nine different genera of mushrooms were collected from different areas of Jazan and Abha belonging to Ascomycotina and Basidiomycotina. The nine genera were Agaricus, Agrocybe, Amanita, Boletus, Coprinus, Lepiota, Pleurotus and Podaxis belonging to Basidiomycotina. Morchella was the only genus belonging to Ascomycotina. The imported mushrooms from different countries mainly Holland, Japan, Malaysia and Thailand are collected from local markets from Abha and Riyadh. Eight genera of edible mushrooms which areidentified as Agaricus bisporus with different varieities like Silver creek and Portobello, Auricularia polytricha (Black fungi), Cyclocybe aegerita (Yanagi Mushroom), Flamullina velutipes, Hypsizygus tessellates (White Crab Mushroom), Lentinula edodes (Shiitake Mushroom), Lyophyllum shimeji (Brown Shimeji), Pleurotus or Oyster Mushroom with two species Pleurotus eryngii and Pleurotus ostreatus. Agaricus was the most common and predominant genera both as local and imported variety. Photographs of the mushrooms were taken and also the cross sections were studied. The structure of the gills is depicted by the spore print taken on the filter paper. More mushroom farms are required to be established so that they can be grown locally. As they are primary decomposers of organic matter they are also responsible for protection of environment and hence agents for controlling pollution. They are also eco friendly agents for recycling the waste.

Biochar and hydrochar from waste biomass promote the growth and enzyme activity of soil-resident ligninolytic fungi

Biochar (BC) and hydrochar (HC) are carbonaceous products obtained through, respectively, pyrolysis and hydrothermal carbonization processes of biomass. Both materials are multi-functional soil amendments. Ligninolytic fungi are primary decomposers of recalcitrant lignocellulosic material in nature through their extensive hyphal network and enzymes. In this work, two BC samples from red spruce pellets (BCSP) and grapevine pruning residues (BCGV) and two HC samples from urban pruning residues (HCUP) and the organic fraction of solid urban wastes (HCSU) were tested at concentrations of 0.4% and 2% (w/v) on the growth and enzyme activity of Trametes versicolor, Pleurotus ostreatus and Pleurotus eryngii. In all treatments with the lower concentration, BC and HC significantly stimulated fungal growth (up to about 90% increase for HCSU on T. versicolor), whereas at the higher dose some inhibition was observed on T. versicolor by BCSP and P. ostreatus by BCSP, BCGV and HCUP. The two materials, especially HC, at both doses noticeably increased the activity of laccase from T. versicolor and P. eryngii, up to 21 and 13 times, respectively, for HCUP compared to controls. The activity of manganese peroxidase from P. ostreatus was also greatly stimulated by BC and HC, especially when added at the higher concentration. The overall results obtained in this study suggest potential benefits for ligninolytic fungi from the presence of these materials in soil at adequate dose of application.

Understory ferns alter soil carbon chemistry and increase carbon storage during reforestation with native pine on previously degraded sites

Reforestation with native species and resulting understory succession can exert important influences on soil organic matter (SOM) storage and chemistry, but a mechanistic understanding of these effects is lacking. We studied different aged Masson pine (Pinus massoniana L.) plantations with and without the understory fern, Dicranopteris dichotoma (Thunb.) Berhn., in subtropical China to assess how SOM over a 30 year sequence of pine growth and fern expansion. To do this, we measured total SOM, lignin-derived phenols, soil carbon (total C and 13C), soil nitrogen (total N and 15N), and soil microbial community composition via phospholipid fatty acid (PLFA) analyses. We found that the accumulation of newly-formed SOM outweighed decomposition of old SOM, with the majority of this increase being derived from fern detrital inputs. Where ferns were present, ferns contributed 54–61% of total soil C storage in surface (0–10 cm depth) soils, which was 62–91% higher than pre-reforestation soil C storage. We found that the abundance of lignin-derived compounds was lower in fern dominated soils, perhaps because soils under ferns supported more soil fungi, the primary decomposers of the lignin in soil. Fern soils also showed higher ratios of syringyls to vanillyls and decreased δ13C values, an indicator that ferns altered the composition of SOM at the molecular level while contributing significantly to SOM accumulation. Reforestation especially when accompanied by fern expansion also improved soil N and phosphorus (P) status, with observed declines in soil δ15N in fern dominated soils aligning with increased nutrient retention and observed increases in soil C storage. Our study highlights the potentially important role of understory ferns in mediating SOM chemistry and soil C storage during ecosystem recovery.