1. Introduction

2. Materials and methods

3. Results and discussion

4. Conclusions

Acknowledgements

Appendix A. Supplementary data

References

Abstract

Soil organic matter (SOM) or humus is essential for the agricultural and environmental functionality of soils. Humus comprises small-size heterogeneous organic molecules arranged in complex meta-stable suprastructures, whose composition can be greatly affected by land management. Here, we report the molecular dynamics of the fractions extracted from an agricultural soil cropped with wheat after one and three years of tillage. The total molecular components, named Humeome, of soil under wheat found in both hydrosoluble and organosoluble fractions isolated by the Humeomic procedure, as determined by GC–MS and high-resolution Orbitrap LC–MS, were compared to the Humeome characterized in the same soil when cropped with maize. While the three-years tillage did not vary the total soil organic carbon under both wheat and maize, the carbon recovered for the sum of Humeomic fractions isolated from soil was significantly larger for maize than for wheat, thus suggesting a general destabilization of SOM under wheat cropping. Moreover, the soil Humeome under wheat resulted more hydrophilic than under maize. While fatty acids and carbohydrates were periodically replenished by crop residues, nitrogen-containing molecules, such as amides and heterocyclic nitrogen, and iron-bound molecular systems were the SOM components mostly reduced under wheat. The losses of these compound classes from the soil Humeome was possibly attributed to the exudation differences between wheat and maize cropping. These results reveal that the molecular dynamics and stability of SOM molecular components can be controlled by crops even in a short term.

Introduction

World soils contain the greatest reservoir of organic carbon (OC) in the biosphere (Batjes, 2014), and innovative measures to reduce OC losses from soils are required to limit global changes (Minasny et al., 2017; Piccolo et al., 2018). Nevertheless, agriculture intensification to produce food for an increased population will inevitably put soil at risk of SOM degradation and fertility losses (Lal, 2009), thus menacing human sustainability on the planet. Due to the still large uncertainty in strategies to sequester OC in soil (Baveye et al., 2018), there is an urgent need to enlarge knowledge on SOM dynamics, in order to control soil OC and prevent degradation of soil fertility.

Humus represents the metabolic substrate for soil microbial activity that, in turn, continues to transform the bioavailable humic pools until a new equilibrium is established between microbial communities, humic matter and plant species (Basler et al., 2015). While the concept of ecological succession was introduced as a theory (Putnam, 1994), few reports were so far published on the molecular changes of humus due to plant species, even though plant rhizodeposition is reckoned to play an important role in OC turnover in soil (Hütsch et al., 2002; Wang et al., 2006). Larger microbial and CO2-C exudates were reported in wheat than in maize (Marx et al., 2007), while wheat residues were found to rapidly and persistently stimulate a microbial degradation of fresh organic matter (Bernard et al., 2007), thereby enhancing mineralization of rhizospheric SOM (Schenck zu Schweinsberg-Mickan et al., 2012).

1- Introduction

2- Material and methods

3- Results

4- Discussion

5- Conclusion

References

Abstract

Soil microbes play vital roles in energy flow and nutrient cycling and, thus, are important for agricultural production. A better understanding of the complex responses of microbial communities to various organic and inorganic fertilization regimes is critical for sustainable development of agroecosystems. Changes in bacterial and fungal abundance and diversity in fluvo-aquic soil in Northern China were studied under 38-year long-term fertilization strategies: four chemical-fertilization strategies (i.e., no fertilizer, N, NP, or NPK), with or without manure amendment, were investigated by high-throughput sequencing and quantitative polymerase chain reaction-based amplification of bacterial 16S rRNA and fungal internal transcribed spacer (ITS) rRNA genes. Chemical fertilizer plus manure addition clearly increased the soil fertility and was recommended for further optimization of fertilization patterns. Both principal component analysis and partial least-square discriminant analysis showed greater impacts of manure addition than chemical fertilizer on bacterial community distributions, whereas fungal communities were more sensitive to inorganic fertilizer. The linear discriminant analysis effect size method revealed that the number of responding microbes (microbes significantly affected by various fertilizations) in bacterial communities in manure-treated soils was markedly higher than that in chemical fertilizer-treated soils, whereas those of fungal communities showed the opposite trend. In addition, redundancy analysis further illustrated the primary importance of organic matter in shaping community distributions of bacteria, rather than in driving fungal community patterns. These results suggested that organic and inorganic fertilizers, respectively, dominated in shaping bacterial and fungal community distributions in fluvo-aquic soils.

Introduction

Soil microorganisms play vital roles in the maintenance of soil health, productivity, and sustainability, and thus crop production, because of their contributions to soil nutrient transformation, formation and decomposition of organic matter, and stabilization of soil aggregates (Van Der Heijden et al., 2008; Zhao et al., 2014; Singh, 2016; Pan et al., 2018a). Therefore, a profound understanding of soil microbial ecology has become increasingly recognized and emphasized because of the ecological and economic importance of microorganisms (Mele and Crowley, 2008). Due to the increasing concerns regarding food demands and the scarcity of land available for agriculture, high amount of fertilizer is implemented to increase crop productivity (Inselsbacher et al., 2010). The application of organic and inorganic fertilizers can cause detectable changes in nutrient availability to plants, as well as in the diversity and function of microorganisms (Marschner et al., 2003). For example, long-term field experiments involving polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE) demonstrated the importance of balanced fertilization in promoting the activities of bacterial communities (Chu et al., 2007a,b; Luo et al., 2015). Nitrogen (N) is regarded as a key limiting factor for soil microbes, and N amendment can alter the activity and diversity of soil organisms (Sarathchandra et al., 2001; Xu et al., 2017; Liu et al., 2019). Organic fertilization exerted no effects on the fungal biomass, while increasing the bacterial biomass by increasing soil organic carbon (Corg) and C/N ratio (Crecchio et al., 2001; Marschner et al., 2003). In addition, manure application promoted soil bacterial communities by enhancing root exudates and also improved plant growth (Bittman et al., 2005). Suzuki et al.

1- Introduction

2- Material and methods

3- Results

4- Discussion

5- Conclusions

References

Abstract

Hydrodynamic fluctuations can trigger sediment suspension concomitantly with internal phosphorus release, while the interactive effect of turbulence mixing and sediment suspension on the regulation of phosphorus dynamics is in need of deep understanding. This study addressed the changes in total phosphorus (TP), phosphate (PO43–P) and suspended sediment (SS) in the overlying water, and measured the profile of dissolved oxygen (DO), Fe(II) and soluble reactive phosphorus (SRP) across the sediment-water interface in the simulated environmental turbulence scenario, For a turbulence intensity (ε) of 3.6 × 10−3 m2/s3, the SRP flux increased hence PO43–P showed a 36.36% increase relative to its initial level. Although ε of 1.3 × 10−2 m2/s3 benefited the delivery of oxygen from the bulk aqueous phase to the upper sediment which can trigger the formation of Fe oxides and hydroxides, the turbulence-induced phosphorus diffusion from the sediment exceeded its inactivation and resulted in a large SRP flux. However, a protion of the released PO43–P can be immobilized through SS adsorption and biotic (likely cyanobacteria) assimilation. Higher turbulence intensities (ε of 3.3 × 10−2 and 7.4 × 10−2 m2/s3) led to an approximately 40-fold increase in TP concentration and a significant increase in sediment suspension, which contributed to the immobilization of a majority of the phosphate through adsorption; thus, the PO43–P concentrations in the overlying water displayed 47.75% and 41.67% decline, respectively. This study also confirmed the sequential phosphorus buffer mechanisms associated with increasing turbulence intensities. With an ε of 3.6 × 10−3 m2/s3, bounding to Fe ion had a significant impact on phosphorus inactivation but with an ε of 7.4 × 10−2 m2/s3, the main immobilization mechanism is switched to phosphorus adsorption from the large quantity of suspended sediment.

Introduction

Phosphorus is essential for the support of phytoplankton growth and is a major driving force for water eutrophication (Søndergaard et al., 2013; Conley et al., 2009). Sediment can act as a sources of pollutants in aquatic environments, and the pollutants accumulated in the sediments can be released into the overlying water, contributing a considerable quantity of phosphorus to the water column (Zhang et al., 2018). For most eutrophic waters, the upper 0e10 cm sediment layer typically has much higher phosphorus levels than that is found in the lower sediment layers; and the most heavily contaminated sediment layer is the top 0e5 cm (Tang et al., 2019), where phosphorus is mobile and can be easily released into the overlying water due to changes in the physicochemical characteristics of the water (Soto-Jimenez et al., 2003; Wu et al., 2001). Thus, even if phosphorus input is effectively reduced, the eutrophication level may remain relatively high, as internal phosphorus loading from sediments may lead to algae blooming and cause a decline in the water quality (Huser and Pilgrim, 2014; Yin et al., 2018; Yin et al., 2016). Therefore, understanding the process of phosphorus release from the sediments is crucial for the management and recovery of eutrophic waters.

Abstract

The root growth of most crop plants is inhibited by soil salinity. Roots respond by modulating metabolism, gene expression and protein activity, which results in changes in cell wall composition, transport processes, cell size and shape, and root architecture. Here, we focus on the effects of salt stress on cell wall modifying enzymes, cellulose microfibril orientation and non-cellulosic polysaccharide deposition in root elongation zones, as important determinants of inhibition of root elongation, and highlight cell wall changes linked to tolerance to salt stressed and water limited roots. Salt stress induces changes in the wall composition of specific root cell types, including the increased deposition of lignin and suberin in endodermal and exodermal cells. These changes can benefit the plant by preventing water loss and altering ion transport pathways. We suggest that binding of Na+ ions to cell wall components might influence the passage of Na+ and that Na+ can influence the binding of other ions and hinder the function of pectin during cell growth. Naturally occurring differences in cell wall structure may provide new resources for breeding crops that are more salt tolerant.

Introduction

Plant evolution has resulted in a large array of mechanisms to tolerate the stresses associated with increased soil salinity. However, for most cereal crops the growth of roots is disrupted when soil salinity exceeds 4 dS/m, equivalent to about 40 mM NaCl. Increased soil salinity exposes plants to ionic sodium (Na+) and chloride (Cl−), which leads to a cascade of responses in the plant due to the ionic and osmotic components of salt stress [1,2].

Salt stress can indirectly affect cell wall properties by causing changes in gene expression, but Na+ can also physically interact with the cell wall components directly, and change their chemical properties [3]. An increase in soil salinity results in accumulation of Na+ in the apoplast, which can lead to an increase in interactions between Na+ and negatively charged sites within cell wall polymers, and also influence apoplastic pH. Salinity causes transient alkalinisation of the apoplast, and this could limit growth in the context of the acid growth theory [4,5]: Auxin activates plasma membrane H+-ATPases and protons are extruded into the apoplast, apoplastic acidification induces cell wall loosening by activating expansins and other remodelling enzymes resulting in loosening of the cell wall. Hence, growth could be limited by a decrease in free apoplastic protons causing a shift in the apoplastic pH away from the range that favors cell-wall loosening [4], although in maize the inhibition of growth as a result of salinity was not associated with the capacity of the epidermal cells to acidify their walls [6].

Systematic mapping of the chemical environment of urban areas from around the world has demonstrated the strong impact of urbanisation on topsoil geochemical distributions originally controlled by the underlying parent material (PM). The variance of some elements including As, Ba, Ca, Cr, Cu, Mo, P, Pb, Sb, Se, Sn and Zn in urban domains appears to be impacted by a mixture of geogenic and anthropogenic controls. This study evaluates how soil chemistry has been influenced by different eras of urbanisation within London and other UK urban areas using (a) the pre-1940 Dudley Stamp First Land Utilisation Survey data and (b) the modern urban domain principally defined by the aggregate classes of the 2007 Land Cover Map. In the London area, calcium, and possibly a substantial proportion of Cu, Pb, Sn and Zn enrichment observed in soils impacted by pre-1940 urbanisation relative to soils impacted only by post-1940 urbanisation, may be partly related to the destruction of buildings during the period 1940–1941 rather than from the disposal or aerial dispersion of coal ash from domestic fires. Some Pb, Cu, Sb, Sb, Sn and Zn contamination appears to be caused by road traffic (leaded petrol and brake dust). The relationships between pre- and post-1940 urbanised areas in London also characterise most of 20 other urban centres in England and Wales for which BGS holds soil chemistry data.

Introduction

Whilst parent material (PM) is the primary geogenic control for some chemical elements in urban areas (Appleton and Adlam, 2012; Appleton et al., 2013), the variance of many elements including As, Ba, Ca, Cr, Cu, Mo, P, Pb, Sb, Se, Sn and Zn in urban domains appears to be impacted by a mixture of geogenic and anthropogenic controls which have developed over different eras of urbanisation. Sources of anthropogenic contamination in urban areas include industrial manufacturing and processing, power and waste incineration plants, domestic coal burning including the historic disposal of ash, emissions from vehicles (especially from the use of leaded petrol), fertilizer use, dispersion of Pb and other metals together with cement, concrete and bricks from demolition and construction including the use of building and demolition waste material for land reclamation and the creation of artificial ground (Albanese and Breward, 2011). The highest levels of contamination are to be expected in areas with the longest history of urbanisation. Preliminary assessments of the topsoil chemistry of the predominantly urban Greater London Authority (GLA) area are available in BGS (2011), Knights and Scheib (2011), Scheib et al. (2011), Ferreira et al. (2017). Lark and Scheib (2013) used model-based analysis, cokriging and Wald statistics to examine how land use recorded at soil sample sites within the Great London Authority (GLA) area accounts for variations in soil Pb concentrations. McIlwaine et al. (2017) reporting on the relationship between potentially toxic element (PTE) concentrations and historical urban development in the soils of Belfast and Sheffield concluded that different PTEs are associated with different periods of development and that soil pollution can be linked to diffuse contamination from road traffic, domestic fuel combustion and industrial processes. The study reported here focusses on processes causing widespread dispersion of contaminants rather than local sources such as industrial manufacturing or waste incineration plants. In particular, we assess whether the different eras of urbanisation in the UK have resulted in significantly different concentrations of elements in surface soils once the confounding influence of parent material (geology) has been eliminated.

Abstract

This research focuses on the heavy metal contamination of the paddy soils and rice from Kocˇani Field (eastern Macedonia) resulting from irrigation by riverine water impacted by past and present base-metal mining activities and acid mine drainage. Very high concentrations of As, Cd, Cu, Pb and Zn were found in the paddy soils (47.6, 6.4, 99, 983 and 1,245 lg g-1 ) and the rice (0.53, 0.31, 5.8, 0.5 and 67 lg g-1 ) in the western part of Kocˇani Field, close to the Zletovska River, which drains the mining facilities of the Pb–Zn mine in Zletovo. In terms of health risk, the observed highest concentrations of these elements in the rice could have an effect on human health and should be the subject of further investigations.

Introduction

Base-metal mining together with milling and grinding operations, concentrating ore and the disposal of tailings along with the acid mine and mill wastewater are some of the most important sources of heavy metals in the environment (Adriano 1986). Therefore, elevated concentrations of heavy metals can be found in and around abandoned and active mines due to the discharge and dispersion of mine waste materials, including tailings and acid mine drainage effluents into nearby agricultural soils, food crops, riverine water and stream sediments (Jung 2001; Korre et al. 2002; Lee et al. 2001; Liu et al. 2005; Lu and Zhang 2005; Simmons et al. 2005; Witte et al. 2004; Wong et al. 2002; Yang et al. 2004). It is well known that heavy metals in agricultural soils can influence both crop yield and quality, and soil containing various elements is a primary nutrient medium for plants. Food crops grown in contaminated areas may accumulate much higher than normal amounts of heavy metals, which may pose a significant public health risk to the local community.

Abstract

Humic acid was isolated from three contrasting organicrich soils and acid-base titrations performed over a range of ionic strengths. Results obtained were unlike most humic acid data sets; they showed a greater ionic strength dependency at low pH than at high pH. Forward- and backtitrations with the base and acid revealed hysteresis, particularly at low pH. Previous authors attributed this type of hysteresis to humic acid aggregates;created during the isolation procedure;being redissolved during titration as the pH increased and regarded the results as artificial. However, forward- and back-titrations with organic-rich soils also demonstrated a similar hysteretic behavior. These observations indicate (i) that titrations of humic acid in aggregated form (as opposed to the more usual dissolved form) are more representative of the acid-base properties of humic acid in soil and (ii) that the ionic strength dependency of proton binding in humic acid is related to its degree of aggregation. Thus, the current use of models based on data from dissolved humic substances to predict the acidbase properties of humic acid in soil under environmental conditions may be flawed and could substantially overestimate their acid buffering capacity.

Introduction

The interactions of humic substances with cations exert a powerful chemical influence in the environment, being important in processes such as pH buffering, metal binding and transport, and nutrient control. The interactions involve both solid-phase material in soils and sediments and dissolved material in natural waters. Humic acid and fulvic acid are usually considered to be the major humic substances involved in cation binding. Broadly speaking, humic acid occurs mostly in soils and sediments as part of the solid phase, while fulvic acid, being more soluble, accounts for a major part of the dissolved organic matter in natural waters (1).

Modern agriculture needs high crop productivity in order to cope with the increasing food demand, and this in order to meet the necessities of the growing world population (Del Buono et al., 2016). In cultivated fields, weeds compete with crops for nutrients and other resources (Gaba et al., 2017). In order to manage this situation, herbicides are used worldwide for crop protection against weeds (Mimmo et al., 2015). However, the massive use of these chemicals can cause resistance in weeds and affect the environment (Gaba et al., 2017). In particular, they can impact on non-target organisms and bring about hazards to human and animal health (Boily et al., 2013; van der Meulen and Singh Chauhan, 2017). Some of these chemicals can also accumulate and persist in soils (Arias-Estevez et al., 2008; Magne et al., 2006 ), and thus could represent a risk for crops in the following cultural cycle (Del Buono et al., 2015). Despite their selectivity in targeting weeds, some herbicides can be phytotoxic to crop species at morphological, physiological and biological levels (Vercampt et al., 2017). Recently, some authors found significant interferences of herbicides on plant mineral nutrition. For example, glyphosate was shown to be able to reduce the uptake of certain micronutrients in soybeans (Zobiole et al., 2010) and sunflower (Eker et al., 2006). In particular, some of these studies showed reductions on iron (Fe) assimilation and distribution in various crop species (Bartucca et al., 2017; Bellaloui et al., 2009; Del Buono et al., 2015; Eker et al., 2006; Ozturk et al., 2008). In general, interferences on the capacity of plants to acquire Fe can result in Fe-chlorosis. This disorder is characterised by interveinal to complete yellowing and browning of leaves which could, in extreme situations, lead to plant death (Singh and Dayal, 1992). Fe has a fundamental role in photosynthesis, DNA and chlorophyll biosynthesis, mitochondrial respiration and nitrogen fixation (Nagajyoti et al., 2010). This element is also a key constituent of many important proteins such as ferredoxin, catalase, peroxidase and superoxide dismutase (Nagajyoti et al., 2010). Therefore Fe is a limiting factor for plant biomass production and quality (Briat et al., 2015).

Antibiotics are widely used in public health and animal husbandry in the treatment and prevention of bacterial infections. The US Food and Drug Administration (FDA) reported that 14.6 million kilograms of annual domestic sales of antimicrobial drugs were used in food-producing animal husbandry in 2014 (FDA. 2014). Particularly, tetracyclines accounted for 71% of these sales. In many countries, the use of antibiotics both for animal disease treatment and growth promotion is unsupervised, which often leads to abuse of antibiotics. Most of veterinary antibiotics were poorly absorbed within the gastrointestinal tract of livestock, causing the presence of biologically active antibiotics in animal waste. It was not unusual to detect high concentrations of antibiotic residues in animal manures (Qiao et al., 2012; Pan et al., 2011;Nordenholt et al., 2016). In an agricultural field at Hannover, the tetracycline (TTC) level in the dried manure from the soil surface was 4 mg/kg (Gerd Hamscher, 2002). Similarly, Martinez analyzed pig manure and turkey dung samples from livestock farms in Austria, Vienna. They revealed that the content of chlortetracycline (CTC), oxytetracycline (OTC), and TTC up to 46 mg/kg, 29 mg/kg and 23 mg/kg respectively (Martinez-Carballo et al., 2007). In China, the antibiotic residues in animal feces are also commonly detected. In a research work, tetracycline antibiotics in feces of livestock breeding farms were investigated in seven provinces. The average content of OTC, TTC and CTC was 5.9 mg/kg, 2.6 mg/kg and 1.3 mg/kg, respectively (ZHANG et al., 2005). Besides, the occurrence of veterinary antibiotics in organic vegetable bases in northern China were analyzed. Strikingly, the highest concentration of antibiotics was up to 183.5 mg/kg for OTC (Hu et al., 30 2010).

The escalation of industrial as well as agricultural enactment substantially the use of pesticides has made our natural resources absolutely sunken and has severely affected the biodiversity and ultimately soil health. Concern has been raised over the long term sustainability and environmental consequences due to intensification of agro-ecosystem. In Punjab, the intensive rice-wheat systems have started to decipher the signs of serious decline associated with loss of soil quality and increased plant health problems [1]. Pesticides enter the soil by direct supplementation (agricultural practices) or by indirect methods (discharge from production sites, accidental spillage, leakage from pesticide dump sites, surface run off, etc.). Pesticides are known to affect the behavior of soil enzymatic system that plays an important role in soil-plant biological activity [2]. The residues of pesticides prevalent in environmental matrices are of larger concern [3]. Fertilizer and pesticide usage tend to elevate the level of nutrients in soil and simultaneously increasing toxins in water and soil. Excessive use of pesticides and fertilizers also pollute the surrounding environment in addition to deteriorating the physical and chemical properties of soil [4]. The usage of such pesticides and fertilizers often leads to a reduction in total microbial activity, porosity, particle and bulk density of soil [4] and excessive leaching of nutrients resulting in salinity induced plant stress [5,6]. Vermicompost on the other hand is basically a complex mixture of fecal matter of earthworm’s humified organic matter and microorganisms. Supplementation of vermicompost in soil or plant growth media leads to increased germination, elevates growth, flowering, and accelerates the production of fruit. Vermicompost helps in maintaining the soil structure healthy by altering the physico-chemical properties of soil [7]. Vermicompost plays an important role in increasing the size, biodiversity and activity of microbes in the soil [4]. It is also a great source of nutrients and organic matter and retains it for a longer period of time without any harmful effect on the environment [8]. It contains high level of plant growth hormones and soil enzymes [9]. Usage of vermicompost may lead to fine tuning of input nutrients and plant needs and thus has maximized yields. Allium cepa is used as a test material to determine genotoxic effects of different chemicals. Environmental agencies like the United Nations Environmental Program, World Health Organization, International Program on Plant Bioassay and US Environmental Protection Agency have advocated and validated the use of plants as test organisms [10]. Allium genus, especially the use of A. cepa for bio-monitoring of genotoxicity is considered to be very efficient [11]. This assay has been utilized to detect genotoxicity of various products like pressmud, waste water sludge, distillery sludge, etc. The present paper has embarked on two major aspects: (i) the effect of pesticides on the genotoxicity of A. cepa and (ii) the effect of vermicompost on A. cepa. This study also focuses on the dynamics of the pesticides present in the agricultural farmlands that are deteriorating the crop quality. Altogether, there is a dire need of a healthy ecosystem that provides with fertile soil, clean water, food and other natural resources [9]. Thus, the evaluation of agricultural soils for detection of their potency to risk biodiversity and ecological systems is obligatory. In this approach the effect of the bioavailable fractions of pollutants/chemicals present in the complex soil matrix was taken into account.

The excessive use of antibiotics for human and veterinary applications results in widespread occurrences of antibiotic resistance bacteria (ARB) and antibiotic resistance genes (ARGs) in the natural environment. Waste water treatment plants (WWTP) receive sewages from different sources, making them possible the hotspots for ARB and ARGs (Guo et al., 2017; Rizzo et al., 2013). As the by-product of WWTP, high abundances of diverse ARB and ARGs have also been documented in dewatered sewage sludge (Li et al., 2013; Guo et al., 2017; Karkman et al., 2017). In contrast to the removal efficiency of ARGs in sewage treatment, their removal in sludge treatment seems less efficient (Yang et al., 2014). Moreover, the sewage sludge containing high organic matter and diverse microorganisms enables the ARGs to propagate and disseminate among bacterial species through horizontal gene transfer (HTG, Li et al., 2013; Guo et al., 2017). The HTG can help spreading the ARGs from commensal and 65 free-living species to pathogenic ones through three canonical modes of conjugation, transformation and transduction, making the ARGs difficult to be completely removed from the environment (Von Wintersdorff et al., 2016). Consequently, to control the ARB and ARGs in sludge, several studies have investigated their fates in different sludge treatment systems (Su et al. (2015; Yang et al., 2016; Zhang et al., 2016; Yang et al., 2014; Wu et al., 2016). Aerobic composting and anaerobic digestion are considered potential recycling methods for treating sludge. However, previous studies showed that the abundance and diversity of ARGs were significantly elevated during thermal composting for sludge (Su et al. (2015; Yang et al., 2016; Zhang et al., 2016). In addition, Su et al. (2015) found 156 unique ARGs and mobile genetic elements in composted sewage sludge.

Many lowland tropical rainforests are strongly phosphorus (P) depleted (Sollins 1998; Mirmanto et al. 1999; Vitousek et al. 2010; Wright et al. 2011) and they harbour some of the highest plant diversity on the planet (Wright 2002). Biotic forces, including plant-associated soil fungi, play a key role in promoting plant diversity (Klironomos 2002; Bell, Freckleton & Lewis 2006; Petermann et al. 2008; Mangan et al. 2010; *Correspondence author. E-mail: jonesfr@science.oregonstate.edu Schnitzer & Klironomos 2011). Fungi interact with plant communities in mutualistic, pathogenic, and commensal ways (Rosenblueth & Mart
ınez-Romero 2006; Smith & Read 2008b; Van Der Heijden, Bardgett & Van Straalen 2008; Dodds & Rathjen 2010). Fungi play critical roles in ecosystem processes including decomposition and nutrient cycling, and they have been hypothesized to play a critical role in the maintenance of plant diversity via pathogen-mediated negative density dependent survival (Janzen 1970; Connell 1971; Augspurger 1983; Clark & Clark 1984; Carson et al. 2008; Timothy Paine et al. 2008; Hol et al. 2013; Bagchi et al. 2014; Comita et al. 2014; but also see Hyatt et al. 2003) and plant-soil feedbacks (Bever 2002; Mangan et al. 2010; Philippot et al. 2013). Despite their recognized role in these processes, the relative importance of the abiotic and biotic drivers of soil fungal community structure and diversity in lowland tropical forests remains poorly understood. Soil properties can determine soil fungal communities and host-microbe interactions (Lauber et al. 2008; Vinale et al. 2008). For example, arbuscular mycorrhizal (AM) fungi (subphylum Glomeromycotina) form associations with 80% of plant species worldwide (Wang & Qiu 2006; Brundrett 2009), and enhance the uptake of water, inorganic P, and other relatively immobile nutrients by effectively increasing root surface area and therefore increasing the volume of soil explored (Smith, Anderson & Smith 2015). The symbiosis between plants and AM fungi can be facultative and dependent on the plant’s soil nutrient requirements and resource availability (Heijden & Kuyper 2001; Lambers et al. 2008; Dumbrell et al. 2009; Albornoz et al. 2016a). Similarly, P and other soil properties can affect non-AM fungal communities, such as ectomycorrhizal fungi (Albornoz et al. 2016b), saprophytic fungi (Kerekes et al. 2013), and pathogens (Toljander et al. 2006; Tedersoo et al. 2016). Nevertheless, fungi are only partially driven by soil properties, and other factors, such as biotic interactions, simultaneously structure fungal communities. Plant communities can also affect their associated fungal communities (Johnson et al. 2004; Prescott & Grayston 2013) due to differences in fungal host specificity, defined as the taxonomic range of plant host species (Molina & Trappe 1982; Botnen et al. 2014). For example, obligate pathogens experience high selection pressure to infect hosts and reciprocal natural selection can occur between hosts and pathogens. This leads to an ‘evolutionary arms race’ between pathogen effectors and plant immunity genes, resulting in increased host specificity of pathogens (Jones & Dangl 2006; Dodds & Rathjen 2010; Brown & Tellier 2011). In contrast, AM fungi are thought to be generalists in forming host associations (i.e. a broad range of hosts; Davison et al. 2015) compared to other fungal groups such as saprophytes, pathogens, and endophytes (Tedersoo et al. 2010). Because of the host specificity that many fungal clades exhibit, they are thought to be strongly coupled with plant communities (Davey et al. 2015; Gao et al. 2015). However, the effects of plant community composition relative to soil chemistry in structuring fungal communities remains largely unknown, and studies that quantitatively determine the relative impact of each are scarce.

Decomposition of detritus plays a crucial role in the recycling of nutrients and organic matter (Swift et al. 1979; Moore et al. 2004). Defined as any resource of nonliving organic matter, detritus is considered the basal trophic level of many terrestrial and aquatic food webs (Swift et al. 1979; Moore et al. 2004; Benbow et al. 2015). In terrestrial ecosystems, detritus may consist of plant-derived matter (e.g. leaf litter, dead wood, root exudates), dead microbes, fecal matter and animal tissue (carrion) (Swift et al. 1979). Plantderived detritus comprises the majority of the resources that undergo decomposition in terrestrial ecosystems but they are nutrient poor and very recalcitrant (Swift et al. 1979; Carter et al. 2007). Contrary, carrion is much more nutrient-rich and decomposes at much faster rates than plant detritus, and, as such, its role in nutrient cycling may be highly relevant (Swift et al. 1979; Barton et al. 2013). Indeed, carrion decomposition is usually associated with the activity of microbes, invertebrate and vertebrate detritivores and scavengers (Carter et al. 2007; Barton et al. 2013). The combined activity of microbes and invertebrates increases the nutrients released from the carrion into the soil; however, vertebrates may reduce this contribution by direct consumption or dispersion (Carter et al. 2007; Barton et al. 2013). In terrestrial ecosystems where carrion releases nutrients into the soil, plants may ultimately mobilize these nutrients entering the belowground detrital pathway (Moore et al. 2004; Carter et al. 2007). Despite its potential importance, only very recently the scientific community has started to acknowledge the role of carrion decomposition in nutrient recycling (DeVault et al. 2003; Carter et al. 2007; Wilson and Wolkovich 2011). Detrital inputs enter any ecosystem via allochthonous or autochthonous sources (Moore et al. 2004). Allochthonous inputs are resources that originate in one habitat but move into another, while autochthonous inputs originate and are consumed in the same habitat (Polis et al. 1997). Many ecosystems experience spatial subsidies as regular seasonal events, but subsidies can also result from sporadic episodes of resource superabundance, named resource pulses (Ostfeld and Keesing 2000; Anderson et al. 2008b; Yang et al. 2008). Examples of resource pulses include periodical cicadas’ emergence in North American forests (e.g. Yang 2004, 2008), El Nin˜o rainfalls in arid ecosystems (e.g. Polis et al. 1997; Meserve et al. 2003; Letnic et al. 2005), seed or fruit mast events (e.g. Woff 1996; Curran and Leighton 2000), and massive spawning events by migratory fish (e.g. Woff and Hershey 1999; Yanai and Kochi 2005). Despite their ecological importance, these studies focused mostly on aboveground processes and just a few assessed belowground effects (Yang 2004; Yang et al. 2010).