Nematodes in Agroecosystems: A Review of Their Role and Influence of Farm Management Practices on the Community Structure

Dependence of soil microbial community structure and function on land use types and management regimes

A trait-based approach in a Mediterranean vineyard: Effects of agricultural management on the functional structure of plant communities

Abstract. Denitrification is an anaerobic respiration process that is the primary contributor of the nitrous oxide (N2O) produced from grassland soils. Our objective was to gain insight into the relationships between denitrifier community size, structure, and activity for a range of pasture soils. We collected 10 dairy pasture soils with contrasting soil textures, drainage classes, management strategies (effluent irrigation or non-irrigation), and geographic locations in New Zealand, and measured their physicochemical characteristics. We measured denitrifier abundance by quantitative polymerase chain reaction (qPCR) and assessed denitrifier diversity and community structure by terminal restriction fragment length polymorphism (T-RFLP) of the nitrite reductase (nirS, nirK) and N2O reductase (nosZ) genes. We quantified denitrifier enzyme activity (DEA) using an acetylene inhibition technique. We investigated whether varied soil conditions lead to different denitrifier communities in soils, and if so, whether they are associated with different denitrification activities and are likely to generate different N2O emissions. Differences in the physicochemical characteristics of the soils were driven mainly by soil mineralogy and the management practices of the farms. We found that nirS and nirK communities were strongly structured along gradients of soil water and phosphorus (P) contents. By contrast, the size and structure of the nosZ community was unrelated to any of the measured soil characteristics. In soils with high water content, the richnesses and abundances of nirS, nirK, and nosZ genes were all significantly positively correlated with DEA. Our data suggest that management strategies to limit N2O emissions through denitrification are likely to be most important for dairy farms on fertile or allophanic soils during wetter periods. Finally, our data suggest that new techniques that would selectively target nirS denitrifiers may be the most effective for limiting N2O emissions through denitrification across a wide range of soil types.

Linking Phyllostachys edulis (moso bamboo) growth with soil nitrogen cycling and microbial community of plant-soil system: Effects of plant age and niche differentiation

Abundance, diversity and functional gene expression of denitrifier communities in adjacent riparian and agricultural zones

Knowledge on the structure and composition of the plant communities has enormous significance in conservation and management of forests. The present study aimed to assess the community attributes, viz., structure, composition and diversity in the moist and dry sal (Shorea robusta) forests in the West Bengal province of India and compare them with the other sal forests of India. The phytosociological data from these forests were quantitatively analysed to work out the species richness, diversity, evenness, dominance, importance value, stand density and the basal area. The analysis showed that plant richness and diversity in moist sal forests of northern West Bengal are higher than the dry sal forests of south-west Bengal; a total of 134 tree (cbh C30 cm), 113 shrub and 230 herb species were recorded in the moist sal forest compared to 35 tree, 41 shrub and 96 herb species in dry sal forest. Papilionaceae was observed to be the dominant family. Dry sal forests had higher tree dominance (0.81) and stand density (1,006 stems ha -1 ) but lower basal area (19.62 m 2 ha -1 ) while moist sal forest had lower tree dominance (0.18) and stand density (438 stems ha -1 ) but higher basal area (56.52 m 2 ha -1 ). Tree species richness and stem density across girth classes in both the types decreased from the smallest to largest trees, while the occurrence rate of species increased with increase in girth class. A t-test showed significant differences in species richness, basal area and the stand density at 95% confidence level (p = \0.05) in the two forest types. The CCA indicated very low overall match (canonical correlation value = 0.40) between the two sets of variables from moist and dry sal types. The differences in these forests could be attributed to the distinct variations in climatic conditions- mainly the rainfall, disturbance regimes and the management practices.

Mycorrhizal fungi are essential for ecosystem functioning. They are the most important pathway of plant-derived C into the soil and facilitate most of the N and P uptake. In boreal and temperate forest ecosystems, the subgroup of ectomycorrhizas is of special significance, and ectomycorrhizal symbiosis is obligatory for a number of tree species. These fungal assemblages can be highly diverse, which is often contrasting with the relatively low number of tree species. This is also true for small monoculture stands, where several studies showed dozens of different ectomycorrhizal species. The elemental mechanisms that drive ectomycorrhizal community composition and structure, especially on larger scales, are still subject of debate. In particular, the role and function of most of the rare species remain largely unknown. In this chapter, we investigate the structural traits of ectomycorrhizal communities of European beech (Fagus sylvatica), one of the most important tree species in temperate deciduous forest ecosystems. We therefore compiled data from ten different beech dominated sites across a European gradient to seek for ubiquitously valid statements regarding the species composition and community structure of ectomycorrhizae. A total of 205 ectomycorrhizal species were detected, of which 45% and 35% could be identified to the species and genus level, respectively. The majority of them are site-specific and found in very low abundances. A few species with narrow host range such as Lactarius subdulcis, Laccaria amethystina or Lactarius pallidus show low abundances on many sites. Three species, namely Hebeloma sinapizans, Lactarius salmonicolor and Elaphomyces aculeatus, appeared to be very dominant on one respective site. Cenococcum geophilum and Russula ochroleuca, both considered multi-host species, occur at all or rather several sites with relatively high abundances. Species ranking-abundance curves revealed a universal distribution pattern, with few dominant ectomycorrhizal species and a long tail of rare species. This shape is regardless of stand age and management practice, though no statistically significant correlations with species richness and the latter mentioned parameters could be found. By looking at several community structures, we were able to add another dimension of rarity and found most of the species not only being rare at a particular site, but also rare in terms of single appearance across several analysed stands. However, a vast part of ectomycorrhizal fungal species still remains unidentified. This circumstance further impedes our understanding concerning the occurrence of rare species. Yet, understanding their functional behaviour is of particular significance, as they could pose a key factor in ecosystem functioning, especially under changing climatic conditions.

Organic management pattern improves microbial community diversity and alters microbial network structure in karst tea plantation

Diazotroph abundance and community structure are reshaped by straw return and mineral fertilizer in rice-rice-green manure rotation

There is increasing emphasis on the need to reduce antimicrobial use (AMU) on dairy farms to reduce the emergence of resistant bacteria which could compromise animal health and impact human medicine. In addition to AMU, the role of farm management is an area of growing interest and represents an alternative route for possible interventions. The aim of this study was to evaluate the impact of farm management practices and AMU on resistances of sentinel bacteria in bulk milk. Dairy farms from two, geographically separate locations within the British Isles were recruited as part of two study groups. Farm management data from study group 1 (n = 125) and study group 2 (n = 16) were collected by means of a face-to-face questionnaire with farmers carried out during farm visits. For study group 2, additional data on AMU was collated from veterinary medicine sales records. Sentinel bacterial species (Enterococcus spp. and E. coli), which have been reported to be of value in antimicrobial resistance (AMR) studies, were isolated from bulk tank milk to monitor antimicrobial susceptibilities by means of minimum inhibitory concentrations (MICs). MIC data for both groups was used to generate an overall “score” for each farm. For both groups, this overall farm mean MIC was used as the outcome variable to evaluate the impact of farm management and AMU. This was achieved through use of elastic net modelling, a regularised regression method which also featured a bootstrapping procedure to produce robust models. Inference of models was based on covariate stabilities and bootstrapped P-values to identify farm management and AMU practices that have significant effects on MICs of sentinel bacteria. Practices which were found to be of importance with respect to Enterococcus spp. included management of slurry, external entry of livestock to the dairy herd, use of bedding materials and conditioners, cubicle cleaning routines and antibiotic practices, including use of β-lactams and fluoroquinolones. Practices deemed to be of importance for E. coli MICs included cubicle and bedding management practices, teat preparation routines at milking and the milking procedure itself. We conclude that a variety of routine farm management practices are associated with MICs of sentinel bacteria in bulk milk. Amendment of these practices offers additional possible routes of intervention, alongside alterations to AMU, to mitigate the emergence and dissemination of AMR on dairy farms.

PurposeFertilization, a widely used agricultural management practice to maximum crop yields, significantly influences microbial community structure and diversity. Soil microbial communities are known to differ across plant growth stages, but how different organic and inorganic fertilization regimes shape microbial temporal variation remains unclear.MethodsTo investigate the temporal stability of microbial communities under organic and chemical fertilization, rhizosphere soil of sorghum was collected at four growth stages (jointing, heading, filling and maturity) in a long-term field experiment with multiple chemical and organic fertilization treatments.ResultsThe results showed that, compared with the control and chemical fertilizer treatments, organic manure treatments resulted in less pronounced variation in microbial community diversity and structure across growth stages. Microbial cooccurrence networks in organic manure treatments were more robust compared to the control and chemical fertilizer treatments, indicating greater stability of microbial community temporal variation in organically fertilized soils. Across different growth stages, fungal communities in manure treatments showed no significant differences in diversity or community structure, and maintained low average variation degree, whereas bacterial communities were more variable.ConclusionThese findings suggest that microbes in organically fertilized soils have more stable communities over time, with fungal communities being more stable than bacterial ones. This study provides insights into how fertilization shapes microbial communities and indicates that organic fertilization enhances the resistance of microbial communities under changing environmental conditions.

Land-use and management practices affect soil ammonia oxidiser community structure, activity and connectedness

Forests are the most dominant land-use type in Louisiana, and timber harvesting is the most economically important of the state’s agricultural commodities. Louisiana has developed voluntary best management practices (BMPs) to minimize negative effects of forest operations on stream water quality, but little is known about how aquatic communities inhabiting low-gradient, headwater streams respond to timber harvesting, and if the current BMPs are effective in protecting community structure and function. In 2005, we initiated a multidisciplinary study in the Flat Creek watershed in central Louisiana to discern the effects of timber harvesting activities, with and without BMP implementation, on benthic aquatic macroinvertebrates. During fall 2007, trees were removed adjacent to two headwater streams in the watershed, and benthic macroinvertebrate samples were subsequently collected at seven stream locations seven times between 2006 and 2009. Our objectives were to describe the community structure of benthic macroinvertebrates in low-order, low-gradient streams, how macroinvertebrate communities responded to timber harvest operations, and whether significant changes in community structure were evident under different levels of BMP implementation. The community structure was predominantly generalist taxa including chironomids, sphaeriid bivalves and asellid isopods. Analyses of variance demonstrated significant increases in bivalve abundance and decreases in the abundance of malacostracan and shredding taxa at most of the sampling sites downstream of BMP-implemented harvest locations in the spring. Additionally, significant increases in bivalves were also found at two sites during late summer. Our results suggest that timber harvesting activities, regardless of BMP implementation, had limited shortterm impacts on resident macroinvertebrates in these lowgradient, subtropical streams. Continued monitoring at the study sites will allow us to better understand the longterm effects of timber harvesting in these stream systems, particularly the resilience of stream biota to harvestingrelated stream conditions.

Soils play a major role in the global carbon cycle and are crucial to the management of climate change. Changes in plant cover derived from different agricultural practices induce variations in the quality of plant residue inputs and in the soil microbial community structure and activity, which may enhance the storage and protection of organic carbon (OC) and nitrogen (N) within aggregates. The aim of this study was to assess how differences in the chemical composition of plant residues in combination with tillage management practices affect the local microbial community activity and structure, and subsequent soil aggregation and OC and N dynamics in an organic, rainfed almond (Prunus dulcis Mill.) orchard. In the laboratory, three types of plant residue (shoots, roots, and the combination of both) coming from different species belonging to each agricultural practice (reduced tillage, reduced tillage plus green manure, reduced tillage plus organic manure, and no-tillage) were mixed with their respective soils and the CO2 released was measured over 243 days at 60% WHC and 28 °C. Water-stable aggregates (including microaggregates within macroaggregates), enzymatic activities related to carbon (dehydrogenase and β-glucosidase) and N (urease) cycling, and the microbial biomass and community structure through phospholipid fatty acid analysis, were measured at the end of the incubation period. Our results indicate that the chemical composition of plant residues controls the microbial community response, mediating decomposition and the incorporation of OC and N in stable aggregates. Therefore, the incorporation of labile and N-rich plant residues into the soil by reduced tillage is recommended since mixing roots and shoots from green manure increased the formation of free micro-aggregates and improved OC and N stabilization in our semiarid agroecosystem.

不同管理模式对温室土壤螨群落结构的影响