Effects of long-term compost and fertilizer application on stability of aggregate-associated organic carbon in an intensively cultivated sandy loam soil

The study examined the influence of compost and mineral fertilizer application on the content and stability of soil organic carbon (SOC). Soil samples collected from a long-term field experiment were separated into macroaggregate, microaggregate, and silt + clay fractions by wet-sieving. The experiment involved seven treatments: compost, half-compost N plus half-fertilizer N, fertilizer NPK, fertilizer NP, fertilizer NK, fertilizer PK, and control. The 18-year application of compost increased SOC by 70.7–121.7%, and mineral fertilizer increased by 5.4–25.5%, with no significant difference between control soil and initial soil. The C mineralization rate (rate per unit dry mass) in microaggregates was 1.52–2.87 mg C kg⁻¹ day⁻¹, significantly lower than in macroaggregate and silt + clay fractions (P < 0.05). Specific C mineralization rate (rate per unit SOC) in silt + clay fraction amounted to 0.48–0.87 mg C g⁻¹ SOC day⁻¹ and was higher than in macroaggregates and microaggregates. Our data indicate that SOC in microaggregates is more stable than in macroaggregate and silt + clay fractions. Compost and mineral fertilizer application increased C mineralization rate in all aggregates compared with control. However, compost application significantly decreased specific C mineralization rate in microaggregate and silt + clay fractions by 2.6–28.2% and 21.9–25.0%, respectively (P < 0.05). By contrast, fertilizer NPK application did not affect specific C mineralization rate in microaggregates but significantly increased that in silt + clay fractions. Carbon sequestration in compost-amended soil was therefore due to improving SOC stability in microaggregate and silt + clay fractions. In contrast, fertilizer NPK application enhanced SOC with low stability in macroaggregate and silt + clay fractions.     

Bacterial populations assimilating carbon from C-labeled plant residue in soil: Analysis by a DNA-SIP approach

In this study, ¹³C-labeled rice callus was prepared as a model material for rice straw and was subjected to a DNA-SIP (stable isotope probing) experiment in which the bacterial population was monitored in a soil sample containing decomposing dried callus. Rice callus (¹³C = 78%) contained the more water-soluble organic carbon and less cellulose and lignin carbon than rice straw. The callus in the soil was 37% decomposed after 56 d of incubation in upland moisture conditions. PCR-DGGE analysis demonstrated that the bacterial community in the soil with the callus changed over time, showing a distinct difference between the first (up to 7 d) and second (14 d and later) stages. After isopycnic centrifugation, DNA in the fractions with a buoyant density between 1.759 and 1.734 g ml⁻¹ was subjected to population analysis (¹³C-assimilating populations). Diverse groups of bacterial sequences were retrieved from the ¹³C-labeled DNA fractions: Actinobacteria, Bacilli, γ-Proteobacteria, Chloroflexi, Sphingobacteria, Flavobacteria, Clostridia, Acidobacteria, Cyanobacteria and Candidate Division. Bacilli were detected mainly in the first stage, and Actinobacteria were detected throughout the incubation period. Several DGGE bands in the light fractions became more prominent in the soil with callus, which suggested that the addition of callus promoted the growth of bacteria that fed on soil organic matter, including α-Proteobacteria, γ-Proteobacteria, Bacilli, Actinobacteria, Nitrospira and Gemmatimonadetes.     

Microbial community composition and carbon cycling within soil microenvironments of conventional, low-input, and organic cropping systems

This study coupled stable isotope probing with phospholipid fatty acid analysis (¹³C-PLFA) to describe the role of microbial community composition in the short-term processing (i.e., C incorporation into microbial biomass and/or deposition or respiration of C) of root- versus residue-C and, ultimately, in long-term C sequestration in conventional (annual synthetic fertilizer applications), low-input (synthetic fertilizer and cover crop applied in alternating years), and organic (annual composted manure and cover crop additions) maize-tomato (Zea mays - Lycopersicum esculentum) cropping systems. During the maize growing season, we traced ¹³C-labeled hairy vetch (Vicia dasycarpa) roots and residues into PLFAs extracted from soil microaggregates (53-250 μm) and silt-and-clay (<53 μm) particles. Total PLFA biomass was greatest in the organic (41.4 nmol g⁻¹ soil) and similar between the conventional and low-input systems (31.0 and 30.1 nmol g⁻¹ soil, respectively), with Gram-positive bacterial PLFA dominating the microbial communities in all systems. Although total PLFA-C derived from roots was over four times greater than from residues, relative distributions (mol%) of root- and residue-derived C into the microbial communities were not different among the three cropping systems. Additionally, neither the PLFA profiles nor the amount of root- and residue-C incorporation into the PLFAs of the microaggregates were consistently different when compared with the silt-and-clay particles. More fungal PLFA-C was measured, however, in microaggregates compared with silt-and-clay. The lack of differences between the mol% within the microbial communities of the cropping systems and between the PLFA-C in the microaggregates and the silt-and-clay may have been due to (i) insufficient differences in quality between roots and residues and/or (ii) the high N availability in these N-fertilized cropping systems that augmented the abilities of the microbial communities to process a wide range of substrate qualities. The main implications of this study are that (i) the greater short-term microbial processing of root- than residue-C can be a mechanistic explanation for the higher relative retention of root- over residue-C, but microbial community composition did not influence long-term C sequestration trends in the three cropping systems and (ii) in spite of the similarity between the microbial community profiles of the microaggregates and the silt-and-clay, more C was processed in the microaggregates by fungi, suggesting that the microaggregate is a relatively unique microenvironment for fungal activity.     

Impacts of different N management regimes on nitrifier and denitrifier communities and N cycling in soil microenvironments

Real-time quantitative PCR assays, targeting part of the ammonia monooxygenase (amoA), nitrous oxide reductase (nosZ), and 16S rRNA genes were coupled with ¹⁵N pool dilution techniques to investigate the effects of long-term agricultural management practices on potential gross N mineralization and nitrification rates, as well as ammonia-oxidizing bacteria (AOB), denitrifier, and total bacterial community sizes within different soil microenvironments. Three soil microenvironments [coarse particulate organic matter (cPOM; >250 μm), microaggregate (53-250 μm), and silt-and-clay fraction (<53 μm)] were physically isolated from soil samples collected across the cropping season from conventional, low-input, and organic maize-tomato systems (Zea mays L.-Lycopersicum esculentum L.). We hypothesized that (i) the higher N inputs and soil N content of the organic system foster larger AOB and denitrifier communities than in the conventional and low-input systems, (ii) differences in potential gross N mineralization and nitrification rates across the systems correspond with AOB and denitrifier abundances, and (iii) amoA, nosZ, and 16S rRNA gene abundances are higher in the microaggregates than in the cPOM and silt-and-clay microenvironments. Despite 13 years of different soil management and greater soil C and N content in the organic compared to the conventional and low-input systems, total bacterial communities within the whole soil were similar in size across the three systems (∼5.15 × 10⁸ copies g⁻¹ soil). However, amoA gene densities were ∼2 times higher in the organic (1.75 × 10⁸ copies g⁻¹ soil) than the other systems at the start of the season and nosZ gene abundances were ∼2 times greater in the conventional (7.65 × 10⁷ copies g⁻¹ soil) than in the other systems by the end of the season. Because organic management did not consistently lead to larger AOB and denitrifier communities than the other two systems, our first hypothesis was not corroborated. Our second hypothesis was also not corroborated because canonical correspondence analyses revealed that AOB and denitrifier abundances were decoupled from potential gross N mineralization and nitrification rates and from inorganic N concentrations. Our third hypothesis was supported by the overall larger nitrifier, denitrifier, and total bacterial communities measured in the soil microaggregates compared to the cPOM and silt-and-clay. These results suggest that the microaggregates are microenvironments that preferentially stabilize C, and concomitantly promote the growth of nitrifier and denitrifier communities, thereby serving as potential hotspots for N₂O losses.     

Tag-encoded pyrosequencing analysis of bacterial diversity in a single soil type as affected by management and land use

Impacts of management and land use on soil bacterial diversity have not been well documented. Here we present the application of the bacterial tag encoded FLX amplicon pyrosequencing (bTEFAP) diversity method, which will promote studies in soil microbiomes. Using this modified FLX pyrosequencing approach we evaluated bacterial diversity of a soil (Pullman soil; fine, mixed, thermic Torrertic Paleustolls) with 38% clay and 34% sand (0–5 cm) under four systems. Two non-disturbed grass systems were evaluated including a pasture monoculture (Bothriochloa bladhii (Retz) S.T. Blake) [P] and a diverse mixture of grasses in the Conservation Reserve Program (CRP). Two agricultural systems were evaluated including a cotton (Gossypium hirsutum L.) -winter wheat (Triticum aestivum L.)-corn (Zea mays L.) rotation [Ct–W–Cr] and the typical practice of the region, which is continuous monoculture cotton (Ct–Ct). Differences due to land use and management were observed in soil microbial biomass C (CRP > P = Ct–W–Cr > Ct–Ct). Using three estimators of diversity, the maximum number of unique sequences operational taxonomic units (OTU; roughly corresponding to the species level) never exceeded 4500 in these soils at the 3% dissimilarity level. The following trend was found using the most common estimators of bacterial diversity: Ct–W–Cr > P = CRP > Ct–Ct. Predominant phyla in this soil were Actinobacteria, Bacteriodetes and Fermicutes. Bacteriodetes were more predominant in soil under agricultural systems (Ct–W–Cr and Ct–Ct) compared to the same soil under non-disturbed grass systems (P and CRP). The opposite trend was found for the Actinobacteria, which were more predominant under non-disturbed grass systems (P and CRP). Higher G? bacteria and lower G+ bacteria were found under Ct–W–Cr rotation and highest abundance of actinomycetes under CRP. The bTEFAP technique proved to be a powerful method to characterize the bacterial diversity of the soil studied under different management and land use in terms not only on the presence or absence, but also in terms of distribution.     

Post-fire mineral N allocation and stabilisation in soil particle size fractions in Mediterranean grassland and shrubland

In the Mediterranean region, long-term post-fire soil N dynamics may be relevant in the stabilisation of soil organic matter and N cycling in the plant-soil system. Post-fire recycling of N may be retained by the retention of N in physically and/or chemically protected fractions of soil organic matter. We studied the allocation of post-fire ¹⁵N-tracer among different soil organic matter fractions (coarse sand, fine sand, coarse silt and fine silt + clay) and ¹⁵N-tracer dynamics for 12 years after prescribed fires in three different Mediterranean plant communities (grassland, mixed shrub-grassland and shrubland). We selected 6 plots for each community and we set experimental fires. Directly after the fires, we applied ¹⁵NH₄⁺-N and we monitored the fate of ¹⁵N-tracer over a period of 12 years. For this purpose, we carried out a physical size fractionation and we analysed the biochemical recalcitrance of N and ¹⁵N by acid hydrolysis in the size fractions obtained. In both burned and unburned plots the finest soil particles (<20 μm) accounted for most soil N. Fire promoted N increases in the medium size fractions while the N pool in the finest and coarsest fractions did not change after the fires. Interestingly, ¹⁵N-tracer was quickly incorporated into fine fractions from which, in the case of plant communities free of legumes, it was remobilised in the following years. Fire did not promote changes in recalcitrant N, but shrubland showed marked decreases in N recalcitrance 6 years after the fires. Despite the fact that the primary effects on soil fractions were detected just after the fires, these persisted for 12 years post-fire. Newly incorporated ¹⁵N-tracer was less recalcitrant than total N and, surprisingly, fine fractions had very low recalcitrant ¹⁵N values, similar to the coarse fractions. Apparently, the N transformations in the finest fraction (<20 μm) were mainly regulated by the quality of the ¹⁵N compounds retained in the fraction.     

Impact of incorporated fresh 13C potato tissues on the bacterial and fungal community composition of soil

Soil microbial communities play a major role in organic matter decomposition, however the importance of the individual species involved is still unclear. To identify the dynamics and identity of bacterial species involved in decomposition of potato tissue as well as the assimilation of carbon from fresh plant material, ¹³C-labeled green potato tissues (¹³C 99.2%) were incorporated in soil microcosm for 39 days at the level of 2.5% (w/dry weight soil). The DNA was extracted from the soil after 1, 6, 15, 25 and 39 days. The heavy (¹³C) and light (¹²C) fractions of DNA were separated by ultracentrifugation and the structures of the bacterial and fungal communities were characterized by DGGE. Primary and secondary ¹³C-sequestrators were identified by sequencing DGGE bands that had appeared only in the heavy DNA fractions. Over the course of the experiment, the most dominant ¹³C-labeled phylogenetic group (class or phylum) was γ-Proteobacteria (51.4%), followed by Actinobacteria (27%), β-Proteobacteria (8.1%) and α-Proteobacteria (5.4%). Two taxa, namely Firmicutes and Verrucomicrobia, were represented by just one sequence type. These bacterial taxa were differentiated into primary (Arthrobacter, Pseudomonas) and secondary sequestrators (Actinobacteria, Dyella, Mesorhizobium and Sphingomonas). The latter were possibly involved in either the redistribution of previously consumed carbon or in a possible degradation of the more complex plant compounds. On the basis of this analysis, only 5 to 8 bacterial taxa were involved in carbon sequestration at any one measured time point. Our results show the importance of specific microbial taxa in the decomposition and mineralization of plant residues in soil, which will allow us to better understand the role of such communities in carbon cycling.     

Effect of land use types on decomposition of 14C-labelled maize residue (Zea mays L.)

The effect of three land use types on decomposition of ¹⁴C-labelled maize (Zea mays L.) residues and soil organic matter were investigated under laboratory conditions. Samples of three Dystric Cambisols under plow tillage (PT), reduced tillage (RT) and grassland (GL) collected from the upper 5 cm of the soil profile were incubated for 159 days at 20 °C with or without ¹⁴C-labelled maize residue. After 7 days cumulative CO₂ production was highest in GL and lowest in PT, reflecting differences in soil organic C (SOC) concentration among the three land use types and indicating that mineralized C is a sensitive indicator of the effects of land use regime on SOC. ¹⁴CO₂ efflux from maize residue decomposition was higher in GL than in PT, possibly due to higher SOC and microbial biomass C (MBC) in GL than in PT. ¹⁴CO₂ efflux dynamics from RT soil were different from those of PT and GL. RT had the lowest ¹⁴CO₂ efflux from days 2 to 14 and the highest from days 28 to 159. The lowest MBC in RT explained the delayed decomposition of residues at the beginning. A double exponential model gave a good fit to the mineralization of SOC and residue-¹⁴C (R² > 0.99) and allowed estimation of decomposition rates as dependent on land use. Land use affected the decomposition of labile fractions of SOC and of maize residue, but had no effect on the decomposition of recalcitrant fractions. We conclude that land use affected the decomposition dynamics within the first 1.5 months mainly because of differences in soil microbial biomass but had low effect on cumulative decomposition of maize residues within 5 months.     

Controls on soil carbon accumulation during woody plant encroachment: Evidence from physical fractionation, soil respiration, and δC of respired CO2

Woody plant encroachment into grasslands and savannas is a globally extensive land-cover change that alters biogeochemical processes and frequently results in soil organic carbon (SOC) accrual. We used soil physical fractionation, soil respiration kinetics, and the isotopic composition of soil respiration to investigate microbial degradation of accrued SOC in sandy loam soils along a chronosequence of C₃woody plant encroachment into a C₄-dominated grassland in southern Texas. Our previous work in this system demonstrated significant changes in the chemistry and abundance of lignin and aliphatic biopolymers within particulate soil fractions during the first 40 yrs of woody plant encroachment, indicating selective accrual of purportedly more recalcitrant plant chemicals. However, during the long-term soil laboratory incubation presented herein, a greater proportion of SOC was mineralized in soils from older woody stands (34-86 yrs) than in soils from younger woody stands (14-23 yrs) and grasslands, providing no evidence for greater biochemical recalcitrance as a controlling mechanism for SOC accrual. In addition, δ¹³C values of respired CO₂ indicate that the mineralized SOC was predominately of C₃ origin from all woody stands along the chronosequence, and that respired CO₂ was primarily derived from the free light fraction (density <1.0 g/cm³) and macroaggregate-sized soil fraction. Our data suggested that the location of SOC among soil fractions was more important than plant polymer chemistry in determining SOC turnover rates during incubation. Surprisingly, estimates of the size and turnover rate of the active SOC pool based on respiratory kinetics did not increase with woody encroachment, and the turnover rate of the slower SOC pool decreased, again supporting the notion that increases in biochemically recalcitrant biopolymers did not hinder decomposition in the lab. These data indicate environmental conditions that may allow for C accrual in the field were alleviated during the controlled incubation. Therefore, C accrual in these sandy loam soils following woody encroachment should not be assumed stable, and this factor should be taken into account when considering responses of SOC to climate change or when making management decisions regarding land cover impacts on SOC.     

Organic matter turnover in soil physical fractions following woody plant invasion of grassland: Evidence from natural C and N

Soil physical structure causes differential accessibility of soil organic carbon (SOC) to decomposer organisms and is an important determinant of SOC storage and turnover. Techniques for physical fractionation of soil organic matter in conjunction with isotopic analyses (δ¹³C, δ¹⁵N) of those soil fractions have been used previously to (a) determine where organic C is stored relative to aggregate structure, (b) identify sources of SOC, (c) quantify turnover rates of SOC in specific soil fractions, and (d) evaluate organic matter quality. We used these two complementary approaches to characterize soil C storage and dynamics in the Rio Grande Plains of southern Texas where C₃ trees/shrubs (δ¹³C=−27‰) have largely replaced C₄ grasslands (δ¹³C=−14‰) over the past 100-200 years. Using a chronosequence approach, soils were collected from remnant grasslands (Time 0) and from woody plant stands ranging in age from 10 to 130 years. We separated soil organic matter into specific size/density fractions and determined their C and N concentrations and natural δ¹³C and δ¹⁵N values. Mean residence times (MRTs) of soil fractions were calculated based on changes in their δ¹³C with time after woody encroachment. The shortest MRTs (average=30 years) were associated with all particulate organic matter (POM) fractions not protected within aggregates. Fine POM (53-250 μm) within macro- and microaggregates was relatively more protected from decay, with an average MRT of 60 years. All silt+clay fractions had the longest MRTs (average=360 years) regardless of whether they were found inside or outside of aggregate structure. δ¹⁵N values of soil physical fractions were positively correlated with MRTs of the same fractions, suggesting that higher δ¹⁵N values reflect an increased degree of humification. Increased soil C and N pools in wooded areas were due to both the retention of older C₄-derived organic matter by protection within microaggregates and association with silt+clay, and the accumulation of new C₃-derived organic matter in macroaggregates and POM fractions.     

Bacterial communities in soil mimic patterns of vegetative succession and ecosystem climax but are resilient to change between seasons

Organism succession during ecosystem development has been researched for aboveground plant communities, however, the associated patterns of change in below-ground microbial communities are less described. In 2008, a study was initiated along a developmental sand-dune soil chronosequence bordering northern Lake Michigan near Wilderness Park (WP). It was hypothesized that soil bacterial communities would follow a pattern of change that is associated with soil, plant, and ecosystem development. This study included 5 replicate sites along 9 soils (n = 45) ranging in age from ∼105 to 4010 years since deposition. Soil bacterial community composition and diversity were studied using bacterial tag-encoded FLX amplicon pyrosequencing of the 16S rRNA gene. Bray–Curtis ordination indicated that bacterial community assembly changed along the developmental soil and plant gradient. The changes were not affected by seasonal differences, despite likely differences in plant root C (e.g. exudates), temperature, and water availability in soil. Soil base cations (Ca, Mg) and pH declined, showing log-linear correlations with soil age (r ∼ 0.83, 0.84 and 0.81; P < 0.01). Bacterial diversity (Simpson's 1/D) declined rapidly during the initial stages of soil development (∼105–450 y) and thereafter (>450 y) did not change. Turnover of plant taxa was also more rapid early during ecosystem development and correlated with bacterial community structural change (P < 0.000001; r = 0.56). It is hypothesized that plants help to drive pedogenic change during early (<450 y) soil development (e.g. pH decline, cation leaching) which drive selection of soil bacterial communities. In mature soils (∼450–4000 y), resilient and stable soil bacterial community structures developed, mimicking steady-state climax communities that were observed during latter stages of primary plant succession. These relationships point to possible feedbacks between plant and bacterial communities during ecosystem development.     

Contributions of soil biota to C sequestration varied with aggregate fractions under different tillage systems

It is increasingly believed that substantial soil organic carbon (SOC) can be sequestered in conservation tillage system by manipulating the functional groups of soil biota. Soil aggregates of different size provide diverse microhabitats for soil biota and consequently influence C sequestration. Our objective was to evaluate the contributions of soil biota induced by tillage systems to C sequestration among different aggregate size fractions. Soil microbial and nematode communities were examined within four aggregate fractions: large macroaggregates (>2 mm), macroaggregates (2–1 mm), small macroaggregates (1–0.25 mm) and microaggregates (<0.25 mm) isolated from three tillage systems: no tillage (NT), ridge tillage (RT) and conventional tillage (CT) in Northeast China. Soil microbial and nematode communities varied across both tillage systems and aggregate fractions. The activity and abundance of microbes and nematodes were generally higher under NT and RT than under CT. Among the four aggregate fractions, soil microbial biomass and diversity were higher in microaggregates, while soil nematode abundance and diversity were higher in large macroaggregates. Structural equation modelling (SEM) revealed that the linkage between microbial and nematode communities and their contributions to soil C accumulation in >1 mm aggregate fractions were different from those in <1 mm aggregate fractions. Higher abundance of arbuscular mycorrhizal fungi (AMF) could enhance C retention within >1 mm aggregates, while more gram-positive bacteria and plant-parasitic nematodes might increase C accumulation within <1 mm aggregates. Our findings suggested that the increase in microbial biomass and nematode abundance and the alteration in their community composition at the micro-niche within aggregates could contribute to the higher C sequestration in conservation tillage systems (NT and RT).     

Culture-dependent and culture-independent microbial investigation of pine litters and soil in subtropical Australia

Background, aim, and scope  Forest plantations, widely grown for wood production, involve the selective promotion of single-tree species or replacement of natural species by exotic tree species. Slash pine (Pinus elliottii) has been chosen for reforestation of infertile sandy soils in southeast Queensland, Australia. These exotic pine plantations minimize soil and water losses and are important scientific study sites. The soil environment of these plantations, though devoid of sufficient nutrients, organic carbon and other factors, harbors innumerable bacteria that may play a crucial role in maintaining soil quality and ecosystem functions. These soil microorganisms also have the potential for use as sensitive biological indicators to reflect environmental changes. It is therefore essential to understand the interrelationships among bacterial communities and their environment by assessing their structural and functional diversity and their responses to disturbances. The main aim of our investigation was to determine the diversity of bacterial communities in forest litters and soil during the forest leaf litter decomposition using culture-dependent and culture-independent techniques. Materials and methods  A 25-cm (diameter) × 40-cm core sample was collected and fractionated into three subsamples designated E1 (L leaf litter layer), E2 (F leaf litter layer), and E5 (0–10 cm soil layer). Both culture-dependent and culture-independent methods were applied in this study. In the culture-independent study, a strategy of whole-community DNA extraction, polymerase chain reaction (PCR) amplification followed by cloning and 16S rDNA sequence analysis was used; for culture-dependent study, the strategy included sample plating and bacteria isolating, DNA extraction, PCR amplification, and 16S rDNA sequence analysis. The diversity similarities between two bacterial communities and two methods are quantified using Jensen–Shannon divergence. Results  From culture-dependent study, 336 colonies in total were isolated and grouped from the three subsamples, and the 16S rRNA sequence analysis from a representative isolate from each morphogroup (21 isolates) indicated that they belonged to the phyla Actinobacteria, Firmicutes, and Proteobacteria. Culture-independent assessment based on 16S rRNA gene library comprising 194 clones revealed that members of the phylum Actinobacteria were absent in the culture-independent studies. Clones in libraries from E1 consisted exclusively of members of the Firmicutes. The majority of clones from E2 were related to Firmicutes (79%) and Proteobacteria (21%). Clones derived from E5 were mostly affiliated with Acidobacterium (42%), followed by unclassified bacteria (27%), Verrucomicrobiales (12%), Proteobacteria (11%), and Planctomycetes (8%). Discussion  This study showed that bacterial culturabilities in different fractions of leaf litters were similar, and both of them were higher than the bacterial culturability in the soil. Unculturable bacterial diversity in the soil, however, was much higher than the leaf litter bacterial diversity. The bacterial diversity on the top layer of leaf litters was slightly less than that on the bottom layer of leaf litters. This might indicate that forest soils are a more complex environment than leaf litters are and also that they might inhabit more unculturable microorganisms in the forest soils, which would need to be further investigated. The leaf litter layer samples also demonstrate the significant difference between the bacterial community diversity discovered by these two methods in this study. The information provided by assessing the different fractions of leaf litters and forest soil has improved our understanding of the bacterial community distributions within the forest soil and the above-leaf litters in an exotic pine plantation of subtropical Australia. Conclusions  This study represents the first attempt to examine the bacterial community in the different fractions of forest leaf litters and soil in subtropical Australia. The data from this study show that the 16S rDNA clone libraries provided more comprehensive phylogenetic diversity in the soil and leaf litter samples than the culture collections provided, and both the culture-dependent and culture-independent studies revealed that the bacterial diversity present in the leaf litters was very different to that present in the soil. The comparative analysis of bacterial communities in different fractions of leaf litters and soil samples has also provided important baseline information about the bacterial diversity and composition in the exotic pine forest plantations. Recommendations and perspectives  The experimental data provided important information on the bacterial diversity in forest leaf litter and soil samples, though additional surveys and comparisons at different locations would be needed to further characterize. In addition, combined methods that can provide different parts of information on bacterial diversity are encouraged to be used in bacterial community study. The established libraries of diverse 16S rRNA gene fragments from slash pine leaf litters and forest soil can be used to construct specific DNA primers and probes to target bacterial groups of interest. It may then be possible to study the ecology of these bacterial communities and the role of specific bacterial groups that contribute to the many interesting properties of these environments.     

Bacterial diversity and community structure along different peat soils in boreal forest

Bacteria in peat forest soil play important role in global carbon cycling. The distribution of bacteria population in different peat soils as a whole and how forest management practices alter the bacterial populations are still poorly known. Using pyrosequencing analysis of 16S rRNA gene, we quantified the diversity and community structure of bacteria in eight peat forest soils (pristine and drained) and two mineral forest soils from Lakkasuo, Finland with either spruce-dominant or pine-dominant tree species. In total, 191,229 sequences which ranged from 15,710 to 22,730 per sample were obtained and affiliated to 13 phyla, 30 classes and 155 genera. The peat forest soils showed high bacterial diversity and species richness. The tree species seems to have more strong impact on the bacterial diversity than the type of peat soil, which drives the changes in bacterial community structure. The dominant taxonomic groups across all soils (>1% of all sequences) were Proteobacteria, Acidobacteria, Actinobacteria, Bacteroidetes, Planctomycetes and Verrucomicrobia. The relative abundance of bacteria phylum and genus differed between soil types and between vegetation. Significant differences in relative abundance of bacteria phyla were only found for Gemmatimonadetes and Cyanobacteria between the pristine and the drained peat forest soils. At genus level, the relative abundance of several genera differed significantly between the peat soils with same or different tree species, including Burkholderia, Caulobacter, Opitutus, Mucilanginibacter, Acidocella, Mycobacterium, Bradyrhizobium, Dyella and Rhodanobacter.     

Chemical and microbial properties in a greenhouse loamy soil after steam disinfestation alone or combined with CaO addition

Steam disinfestation represents an increasingly attractive strategy to control soil-borne pathogens and weeds both in greenhouses and field crops. Beyond pest control, steam injection has the potential to alter soil nutrient dynamics and composition of bacterial communities. This study investigated the impact of a soil-steaming method (the Bioflash™ system) on main chemical (total organic C, TOC; total N, TN; cation exchange capacity, CEC; exchangeable Na, K, Mg and Ca; KCl-extractable ammonium and nitrate, DTPA-exchangeable Mn) and microbial (microbial biomass C, MBC; genetic structure of bacterial communities) properties in a greenhouse loamy soil. Treatments were carried out by using a self-propelled soil-steaming machine operating at two steaming modes (deep or shallow) in combination or not with addition of an exothermically reacting compound (CaO at a 1000 kg ha⁻¹ rate). Soils from a five-treatment (NS, non-steamed soil, DS, deep steam injection; DS + E, deep steam injection plus CaO; SS, shallow steam injection; SS + E, shallow steam injection plus CaO) plot block were sampled before steaming and after 8, 19, 54 and 91 days. Compositional shifts in the structure of soil bacterial communities were monitored by denaturing gradient gel electrophoresis (DGGE) fingerprinting of soil-extracted 16S rRNA gene fragments, using primers specific for Bacteria and Actinobacteria. Maximum soil temperature reached 70 °C (DS) and 82 °C (DS + E) in the 10-20 cm layer; and 50 °C (SS) and 53 °C (SS + E) in the 0-10 cm layer. TOC, TN, CEC, exchangeable Na, Mg and Ca were not statistically affected by soil steaming, CaO addition, depth of injection or their interactions. Conversely, SS promoted a large release of exchangeable K, notwithstanding CaO addition. Steam disinfestation significantly stimulated ammonium release, which further increased in CaO-treated steamed soils. Generally ammonium and nitrate pools varied oppositely, being the latter markedly reduced at the end of the observation period. Available Mn was significantly increased by soil steaming, but it was depressed when steaming was combined with CaO addition. Soil steaming markedly reduced the MBC, especially in DS-treated and SS-treated plots. The genetic structure of soil bacterial and actinobacterial communities was largely unresponsive to the steaming treatments. Even though the Bioflash™ system did not cause bacterial eradication or compositional shifts in bacterial community structure, soil steaming stimulated an increased release of soluble nutrients (K⁺, Mn²⁺, NH₄⁺-N). Over a longer perspective, excessive soil resources exploitation and potential risks of Mn toxicity should be cautiously considered especially in repeatedly (and eventually acid) steamed soils.     

Pineapple–banana rotation reduced the amount of Fusarium oxysporum more than maize–banana rotation mainly through modulating fungal communities

Continuous cropping with banana results in an enrichment of Fusarium oxysporum f. sp. cubense race 4 (FOC) in soil, causing the soil-borne disease Fusarium wilt. Crop rotation has been an effective method of controlling various soil-borne diseases. However, no information is currently available concerning variations in soil microbial community structure in banana crop rotations. Thus, the influence of two-year crop rotation systems of pineapple–banana and maize–banana on the population density of FOC and soil microbial community structure was investigated to identify which rotation system is more effective in FOC suppression and differences in microbial community composition among different rotations. Bacterial and fungal communities were interrogated by pyrosequencing of the 16 S RNA gene and the internal transcribed spacer (ITS) region. The pineapple–banana rotation was more effective than maize–banana in reducing FOC abundances and suppressing Fusarium wilt disease incidence. Allelopathic effects of pineapple root exudates on FOC were not observed. Greater fungal community variations than bacterial were identified between the two rotation systems, suggesting that fungal communities may play a more important role in regulating FOC abundances. Furthermore, in the pineapple–banana rotation, Acidobacteria, Planctomycetes, Chloroflexi phyla, Gp1, Gp2 and Burkholderia bacterial genera increased while the fungal phyla Basidiomycota, (esp. Gymnopilus) increased and Sordariomycetes decreased. Such changes may be important microbial factors in the decrease in FOC.     

Changes in soil organic carbon dynamics in an Eastern Chinese coastal wetland following invasion by a C4 plant Spartina alterniflora

The exotic C₄ grass Spartina alterniflora was intentionally introduced to tidal coastal wetlands in Jiangsu province of China in 1982. Since then it has rapidly replaced the native C₃ plant Suaeda salsa, becoming one of the dominant vegetation types in the coastal wetlands of China. Although plant invasion can change soil organic carbon (SOC) storage, little is known about how plant invasion influences C storage within soil fractions. We investigated how S. alterniflora invasion across an 8, 12 and 14-year chronosequence affected SOC and soil nitrogen (N), using soil fractionation and stable δ¹³C isotope analyses. SOC and N concentrations at 0-10 cm depth in S. alterniflora soil increased during the S. alterniflora invasion chronosequence, ranging from 3.67 to 4.90 g C kg⁻¹ soil, and from 0.307 to 0.391 g N kg⁻¹ soil. These were significantly higher than the values in the Suaeda salsa community, by 27.0-69.6% for SOC, and 21.8-55.2% for total N. The S. alterniflora-derived SOC varied from 0.40 to 0.92 g C kg⁻¹ according to mixing calculations, assuming the two possible SOC sources of S. alterniflora and S. salsa, and accounted for 10.8-18.7% of total SOC in the colonized soils. The estimated accumulative rate of SOC from C₄ (S. alterniflora) was 64.1 C kg⁻¹ soil year⁻¹ and from C₃ sources was 78.1 mg C kg⁻¹. The concentration of S. alterniflora-derived SOC significantly decreased from coarse fraction to fine fraction, and linearly increased as the period of S. alterniflora invasion increased. The highest accumulative rate of SOC from a C₄ source occurred in macroaggregates, while the highest rate from C₃ was in microaggregates. The storage of SOC derived from S. alterniflora in the macroaggregates was 0.27-0.44 g C kg⁻¹ soil, accounting for 43.1-49.1% of the total C₄derived SOC in the soil. Our results suggest that S. alterniflora invasion in coastal wetlands could facilitate SOC storage, because of the high potential for accumulation of the C which has been newly derived from S. alterniflora litter and roots.     

Effects of fertilization with urban and agricultural organic wastes in a field trial – Prokaryotic diversity investigated by pyrosequencing

The impact of different fertilizer treatments on prokaryotic diversity in a Danish urban waste field trial was investigated using tag-encoded amplicon pyrosequencing. The field trial was established in 2003 to investigate the application of urban organic waste as fertilizer in agriculture and to identify the effects on soil quality. The fertilizers (e.g. composted organic household waste, sewage sludge and human urine) contain a large amount of nutrients but possibly also undesirable toxic compounds that may influence the bacterial flora in the soil. A 561 bp fragment of the 16S rRNA gene flanking the V4, V5 and V6 regions, was amplified from each soil sample, tagged and sequenced using pyrosequencing. The major classified bacterial phyla and proteobacterial classes for all treatments were Actinobacteria, Acidobacteria and Betaproteobacteria, while the Crenarchaeota was the most frequent phylum of Archaea. No major changes in the community composition due to different fertilizer treatments were found, demonstrating a high robustness of the soil microbiota. However, some differences were observed e.g. Cyanobacteria were most frequent in the unfertilized soil, in comparison to the soils treated with nitrogen containing fertilizers and Firmicutes had higher occurrence in the soil with the composted household waste compared to all other treatments. Additionally, we used quantitative PCR (qPCR) to quantify specific bacterial groups, and used these numbers to convert the relative abundances of all bacteria obtained by pyrosequencing, to the actual numbers present in one gram of soil. All treatments resulted in a total number of bacteria between 1.99 × 10⁹ and 4.11 × 10⁹ gram⁻¹ soil.     

Soil organic matter and CO2 emission as affected by water erosion on field runoff plots

Soil organic carbon (SOC) is an important component of the global carbon cycle. Its dynamics depends upon various natural and anthropogenic factors including soil erosion. A study on Miamian silty clay loam soil in central Ohio was conducted to investigate the effect of soil erosion on SOC transport and mineralization. Runoff plots 10, 20 and 30 m long on a 7% slope under natural rainfall were used. Total soil loss, evolution of CO₂ from the displaced aggregates of various fractions, and total SOC concentrations were determined. It was shown that the primary ways of SOC loss resulted from two processes: 1) mechanical preferential removal of SOC by overland flow and 2) erosion-induced mineralization. Significant amounts of SOC mobilized by erosion at the upper part of the slope during the season (358 kg ha^? 1) could be lost to the atmosphere within 100 days (15%) and transported off site (44%). Breakup of initial soil aggregates by erosive forces was responsible for increased CO₂ emission. During the initial 20 days of incubation the amount of CO₂ released from coarse size sediment fractions (0.282 g C kg^? 1 soil d^? 1) was 9 times greater than that in fine fractions (0.032 g C kg^? 1 soil d^? 1) due to the greater initial amount of SOC and its exposure to the environment. Sediment size distribution as well as its residence time on the site was the primary controllers of CO₂ loss from eroded soil.     

Incongruous variation of denitrifying bacterial communities as soil N level rises in Canadian canola fields

Soil N fertilization stimulates the activity of the soil bacterial species specialized in performing the different steps of the denitrification processes. Different responses of these bacterial denitrifiers to soil N management could alter the efficiency of reduction of the greenhouse gas N₂O into N₂ gas in cultivated fields. We used next generation sequencing to show how raising the soil N fertility of Canadian canola fields differentially modifies the diversity and composition of nitrite reductase (nirK and nirS) and nitrous oxide reductase (nosZ) gene-carrying denitrifying bacterial communities, based on a randomized complete blocks field experiment. Raising soil N levels increased up to 60% the ratio of the nirK to nirS genes, the two nitrite reductase coding genes, in the Brown soil and up to 300% in the Black soil, but this ratio was unaffected in the Dark Brown soil. Raising soil N levels also increased the diversity of the bacteria carrying the nitrite reductase gene nirK (Simpson index, P = 0.0417 and Shannon index, 0.0181), and changed the proportions of the six dominant phyla hosting nirK, nirS, and nosZ gene-carrying bacteria. The level of soil copper (Cu) and the abundance of nirK gene, which codes for a Cu-dependent nitrite reductase, were positively related in the Brown (P = 0.0060, R² = 0.48) and Dark Brown (0.0199, R² = 0.59) soils, but not in the Black soil. The level of total diversity of the denitrifying communities tended to remain constant as N fertilization induced shifts in the composition of these denitrifying communities. Together, our results indicate that higher N fertilizer rate increases the potential risk of nitrous oxide (N₂O) emission from canola fields by promoting the proliferation of the mostly adaptive N₂O-producing over the less adaptive N₂O-reducing bacterial community.