Community In Field Soil Research Articles

The Addition of a High Concentration of Phosphorus Reduces the Diversity of Arbuscular Mycorrhizal Fungi in Temperate Agroecosystems

Phosphorus (P) is an essential macronutrient crucial for both plant growth and crop production, playing a pivotal role in agriculture since the early 20th century. The symbiotic relationship between AMF and plants serves as a classic illustration. These fungi play a regulatory role in the growth and development of plants, especially in facilitating the absorption of P and carbon molecules by plants. While there has been a growing body of research on the community assembly of arbuscular mycorrhizal fungi (AMF) in recent decades, our knowledge of the processes governing the coexistence of these AMF communities influenced by P in agroecosystems remains limited. To investigate the impact of various P fertilizers on AMF communities in temperate agroecosystems, this study was conducted using soils sourced from wheat–maize rotation farmland at Henan Agricultural University Yuanyang Base. With the Illumina MiSeq high-throughput sequencing technique, we systematically examined the taxonomic composition of soil AMF at the Yuanyang Base of Henan Agricultural University in a wheat–maize rotation agricultural field. Our primary objective was to unravel the mechanisms behind AMF community assembly and stability under varying P gradient fertilization conditions. Nonmetric Multidimensional Scaling (NMDS) analysis revealed significant differences among AMF communities in field soil subjected to various treatments (p < 0.05). A torus translations test demonstrated positive associations with the three treatments in 36 out of the 51 examined AMF operational taxonomic units (OTUs), making up 70.59% (p < 0.05) of the results. Furthermore, 37.84% (14/37) of the OTUs displayed preferences for the low P concentration treatment, while 34.29% (12/35) and 32.26% (10/31) favored medium and high P concentrations, respectively. An analysis of the Normalized Stochasticity Ratio (NST) and Checkerboard Score (C-score) indicated that in temperate agroecosystems, deterministic processes predominantly governed AMF in all treatment groups, with high P conditions exerting a stronger influence than low or medium P conditions. This study underscores the profound impact of long-term P fertilizer application on AMF community structures within temperate agricultural systems employing wheat–maize rotation. Additionally, it highlights the dominant role played by deterministic processes in shaping the assembly of AMF communities in these temperate agricultural systems that use P fertilizers. These findings emphasize the need for balanced nutrient management, particularly concerning P, to ensure the stability of AMF communities.

Triterpenoid and Steroidal Saponins Differentially Influence Soil Bacterial Genera.

Plant specialized metabolites (PSMs) are secreted into the rhizosphere, i.e., the soil zone surrounding the roots of plants. They are often involved in root-associated microbiome assembly, but the association between PSMs and microbiota is not well characterized. Saponins are a group of PSMs widely distributed in angiosperms. In this study, we compared the bacterial communities in field soils treated with the pure compounds of four different saponins. All saponin treatments decreased bacterial α-diversity and caused significant differences in β-diversity when compared with the control. The bacterial taxa depleted by saponin treatments were higher than the ones enriched; two families, Burkholderiaceae and Methylophilaceae, were enriched, while eighteen families were depleted with all saponin treatments. Sphingomonadaceae, which is abundant in the rhizosphere of saponin-producing plants (tomato and soybean), was enriched in soil treated with α-solanine, dioscin, and soyasaponins. α-Solanine and dioscin had a steroid-type aglycone that was found to specifically enrich Geobacteraceae, Lachnospiraceae, and Moraxellaceae, while soyasaponins and glycyrrhizin with an oleanane-type aglycone did not specifically enrich any of the bacterial families. At the bacterial genus level, the steroidal-type and oleanane-type saponins differentially influenced the soil bacterial taxa. Together, these results indicate that there is a relationship between the identities of saponins and their effects on soil bacterial communities.

Survival of a commercial AM fungal inoculant and its impact on indigenous AM fungal communities in field soils

Arbuscular mycorrhizal fungi (AMF) are being promoted as commercial biofertilizers (bioinoculants) for sustainable agriculture. However, little is known about the survival of AMF inoculants in soil and their impacts on indigenous AMF communities under multiple cropping conditions. A three-year study was conducted at four field-sites across semiarid to subhumid climate zones in the Saskatchewan prairie, Canada. A commercial AMF inoculant containing Rhizophagus irregularis was applied at seeding in the first year of the study in 2011 to the host crop pea (Pisum sativum), grown in open-ended soil cores. The persistence of the inoculant and subsequent phylogenetic changes in the community of the indigenous AMF taxa were assessed for three consecutive cropping seasons (2011–2013), during which wheat (Triticum aestivum) was grown in year two and pea in year three. At harvest of each year, the AMF community was assessed using 18S rRNA gene pyrosequencing of AMF trap roots. A total of 131 AMF OTUs (year 1: 54, year 2: 28, year 3: 49 OTUs, respectively), representing eight genera (Glomus, Funneliformis, Claroideoglomus, Diversispora, Paraglomus, Rhizophagus, Septoglomus, and Archaeospora) was detected. Phylogenetic analysis showed the inoculant could be detected to the end of third cropping season (i.e., 27-month after inoculation) at the Swift Current and Outlook field-sites, but was only detected at the Scott and Melfort field-sites to the end of the first (3-month) and second (15-month) growing seasons, respectively. The commercial inoculant caused alterations (taxa suppression, stimulation, and exclusion) of specific members of the indigenous AMF (abundance and diversity) after the first crop season at Swift Current and after all three seasons at Outlook, Scott, and Melfort sites. Multivariate statistical analysis revealed the survival of the commercial inoculant, and the subsequent changes in the indigenous AMF taxa were dependent on soil environments.

Antibiotic resistance genes and bacterial communities in cornfield and pasture soils receiving swine and dairy manures

Land application of animal manure could change the profiles of antibiotic resistant bacteria (ARB), antibiotic resistance genes (ARGs) and bacterial communities in receiving soils. Using high-throughput real-time quantitative PCR and 16S rRNA amplicon sequencing techniques, this study investigated the ARGs and bacterial communities in field soils under various crop (corn and pasture) and manure (swine and dairy) managements, which were compared with those of two non-manured reference soils from adjacent golf course and grassland. In total 89 unique ARG subtypes were found in the soil samples and they conferred resistance via efflux pump, cellular protection and antibiotic deactivation. Compared to the ARGs in the golf course and grassland soils (28 and 34 subtypes respectively), manured soils generally had greater ARG diversity (36–55 subtypes). Cornfield soil frequently receiving raw swine manure had the greatest ARG abundance. The short-term (one week) application of composted and liquid swine manures increased the diversity and total abundance of ARGs in cornfield soils. Intriguingly the composted swine manure only marginally increased the total abundance of ARGs, but substantially increased the number of ARG subtypes in the cornfield soils. The network analysis revealed three major network modules in the co-occurrence patterns of ARG subtypes, and the hubs of these major modules (intl1-1, vanC, and pncA) may be candidates for selecting indicator genes for surveillance of ARGs in manured soils. The network analyses between ARGs and bacteria taxa revealed the potential host bacteria for the detected ARGs (e.g., aminoglycoside resistance gene aacC4 may be mainly carried by Acidobacteriaceae). Overall, this study highlighted the potentially varying impact of various manure management on antibiotic resistome and microbiome in cornfield and pasture soils.

Normal Operating Range of Bacterial Communities in Soil Used for Potato Cropping

In this study, the impacts of six potato (Solanum tuberosum) cultivars with different tuber starch allocations (including one genetically modified [GM] line) on the bacterial communities in field soil were investigated across two growth seasons interspersed with 1 year of barley cultivation, using quantitative PCR, clone library, and PCR-denaturing gradient gel electrophoresis (DGGE) analyses. It was hypothesized that the modifications in the tuber starch contents of these plants, yielding changed root growth rates and exudation patterns, might have elicited altered bacterial communities in the soil. The data showed that bacterial abundances in the bulk soil varied over about 2 orders of magnitude across the 3 years. As expected, across all cultivars, positive potato rhizosphere effects on bacterial abundances were noted in the two potato years. The bulk soil bacterial community structures revealed progressive shifts across time, and moving-window analysis revealed a 60% change over the total experiment. Consistent with previous findings, the community structures in the potato rhizosphere compartments were mainly affected by the growth stage of the plants and, to a lesser extent, by plant cultivar type. The data from the soil under the non-GM potato lines were then taken to define the normal operating range (NOR) of the microbiota under potatoes. Interestingly, the bacterial communities under the GM potato line remained within this NOR. In regard to the bacterial community compositions, particular bacterial species in the soil appeared to be specific to (i) the plant species under investigation (barley versus potato) or, with respect to potatoes, (ii) the plant growth stage. Members of the genera Arthrobacter, Streptomyces, Rhodanobacter, and Dokdonella were consistently found only at the flowering potato plants in both seasons, whereas Rhodoplanes and Sporosarcina were observed only in the soil planted to barley.

Potato cultivar type affects the structure of ammonia oxidizer communities in field soil under potato beyond the rhizosphere

The effects of plants on the microbiota involved in the oxidation of ammonia in soils have been controversial. Here, we investigated the dynamics in the abundances and community structures of the bacterial and archaeal ammonia oxidizers (AOB and AOA, respectively) in two fields that were cropped with potato. Six different potato cultivars were used, including a genetically-modified one, in a fourfold replicated experimental set-up. On the basis of bulk and rhizosphere soil extracted microbial community DNA, AOB and AOA quantitative PCR as well as PCR-DGGE were performed. In addition, samples were used for the production and analysis of amoA gene fragment based clone libraries. Regardless of sample type (bulk versus rhizosphere soil) and across soils, the population sizes of AOA (of the order 104–108amoA gene copies g−1 dry soil), were generally higher than those of AOB in the same samples (about 104–105 g−1 dry soil), resulting in ratio's of log-transformed values > 1.0. Whereas the AOB numbers were generally raised in the rhizosphere versus bulk soils in both soils, the opposite was true for the AOA numbers. Moreover, significant effects of cultivar type on both the AOB and AOA community structures were found in both soils, and these extended to beyond the rhizospheres. The effects were found across the whole growth season. Soil type did not significantly affect the community structures of AOA, but had a small effect on the community structure of AOB. Analysis of the structures of the AOB communities revealed a prevalence of AOB subgroups 2, 3a, 3b and 4 in one field soil and of 2 and 4 in the other one. With respect to the AOA, soil/sediment clusters (SS) I, II, III and IV were found to prevail.

Microbial communities in sugarcane field soils with and without a sugarcane cropping history

Microbial communities in rhizosphere soil from sugarcane (Saccharum inter-specific hybrids) and bulk soil were compared at paired field sites with and without a sugarcane cropping history to determine whether monoculture affects soil microbial community composition. Differences were evaluated for culturable microorganisms and functional diversity indicated by community level physiological profiles (CLPP). Qualitative differences in rhizosphere bacterial communities were detected between sites with no sugarcane cropping history (Nsite) and sites with a long-term sugarcane cropping history (Lsite). More fluorescent pseudomonads were detected in Nsite than Lsite rhizosphere soil at two of three sites, and Actinobacteria were more numerous in Nsite than Lsite rhizosphere soil at one site. Fusarial fungi were more numerous in Nsite than Lsite rhizosphere soils. Bacteria were more numerous in rhizosphere soil compared to bulk soil. Total bacterial, pseudomonad, and Actinobacteria population densities were greater in bulk soil from an Nsite compared to an Lsite. CLPP distinguished bulk from rhizosphere soil at one of two sites and Nsite and Lsite rhizosphere soils at two of four sites. Site affected CLPP similarity more than cropping history. The results demonstrated that sugarcane monoculture can affect the composition of the microbial community in field soil. The findings have possible implications for reduced yields associated with sugarcane monoculture.

Shifting the balance from qualitative to quantitative analysis of arbuscular mycorrhizal communities in field soils

Population studies of arbuscular mycorrhizal fungi (AMF) have traditionally been achieved by indirect analyses of soil-borne spore populations. These studies are not necessarily reflective of populations of AMF within the roots. Advances in molecular biology have revolutionized the analysis of fungal populations colonizing roots and forming mycorrhizas. Initially these studies were qualitative and reported presence or absence of particular AMF species in soils or in roots for comparison between different environments. More recently, the methodology has developed for direct quantification of AMF within roots. Quantitative PCR provides the means to study spatial distribution and individual quantification of AMF in mixed communities over time. In this review, we discuss the progress and application of indirect, direct and finally quantitative methodologies for studying arbuscular mycorrhizal communities. We conclude that the molecular tools now exist to quantitatively analyse the effect of environment, management or inoculation of soils on AMF communities within roots.

Field investigations on the survival of Escherichia coli and presence of other enteric micro-organisms in biosolids-amended agricultural soil

To measure the survival of enteric micro-organisms in agricultural soil amended with conventional and enhanced treated biosolids in relation to environmental and edaphic conditions. Escherichia coli, Salmonella and F-specific RNA bacteriophage were enumerated in sludge and amended soil. Salmonella was not detected and only small numbers of bacteriophages were found in conventional, dewatered mesophilic anaerobically digested biosolids (DMAD). Neither organism was detected in soil. Escherichia coli numbers in soil increased with DMAD application compared with the unamended control, or soil receiving enhanced treated, thermally dried digested (TDD) and composted (CPT) biosolids. Empirical statistical models were developed summarizing the relationship between soil temperature, moisture content and time and E. coli populations. Background numbers of E. coli declined with increasing soil temperature and decreasing soil moisture responding to seasonal patterns in environmental conditions. Time following application was the only significant explanatory variable of E. coli numbers and decay in DMAD-amended soil. E. coli are an indigenous component of the microbial community in field soil and populations increased in cool, moist soil during autumn-winter and declined in warm, dryer soil during spring-summer. Enhanced treated biosolids were not a source of E. coli, but reduced the size of the indigenous population possibly by stimulating the activity of predatory and competing soil flora because of the organic substrate input from sludge. Conventionally treated biosolids increased E. coli numbers in soil. However, introduced bacteria declined rapidly and survival was limited to 3 months, irrespective of the timing of sludge application or environment. The results provide assurance that residual numbers of pathogens applied to soil in treated biosolids decay to background values well within cropping and harvesting restrictions imposed when sewage sludge is spread on farmland.

Influences of organic and synthetic soil fertility amendments on nematode trophic groups and community dynamics under tomatoes

Research was conducted to examine the effects of organic and synthetic soil amendments and tillage on nematode communities in field soils planted to tomato ( Lycopersicon esculentum) at two locations. The experimental design was a replicated split plot with chisel-plow tillage and bare-soil or chisel-plow tillage and surface mulch with wheat straw as main plots, and soil amendments of synthetic fertilizer, composted cotton-gin trash, swine manure, or a rye-vetch green manure as subplots. Tillage did not affect free-living or plant-parasitic nematode community dynamics, but soil amendments had a large impact on nematode community structure and diversity. Populations of bacterivorous nematodes mainly in the Rhabditidae and Cephalobidae, and fungivorous nematodes were greater after planting in soils amended with swine manure, composted cotton-gin trash, or rye-vetch, than in soils amended with synthetic fertilizer at both locations. Populations of nematodes in these trophic groups decreased through time in each year. Populations of Meloidogyne incognita in soil were not affected by soil amendments, but increased through time at each location. Root-gall indices were lower in plots containing swine manure or cotton-gin trash than in those with synthetic fertilizer or rye-vetch during the second season. The combined nematode maturity index values were greater at planting in soils amended with rye-vetch or fertilizer than in soils with swine manure and composted cotton-gin trash. Shannon’s diversity index decreased over time for both years at one location, regardless of soil amendment. At the second location, the Shannon’s diversity index decreased only in the second year. Use of descriptive indices, including the Enrichment index, structure index, and channel index provided useful information about the effects of organic amendments on the structure of nematode communities in tomato field soils.

Biodiversity of arbuscular mycorrhizal fungi in agroecosystems

Arbuscular mycorrhizal fungi [AMF] are soil fungi which form a mutualistic symbiosis with the roots of plants. A variety of benefits to the host have been ascribed to mycorrhizae, most often enhanced uptake of immobile nutrients from the soil, notably P. An understanding of the impacts of agronomic practices upon communities of these fungi would help to ensure an opportunity for the utilization of the symbiosis and contribute to the success of sustainable agriculture. Measurement of the diversity of AMF communities in field soils presents a variety of challenges, among them the difficulty of identifying field collected spores, the detection of non-sporulating members of the community, and the lack of relation between functional diversity and the morphological diversity of spores used to delineate species. These challenges, as well as current efforts to overcome them, are discussed and recent research elaborating the effects of agromonic practices upon AMF communities and the effectiveness of mycorrhizae is presented.