Microbes Associated to Dyer’s woad (Isatis tinctoria L.): Pigment Extraction, Dyeing and Cultivation with Non-toxic Inputs. A Review

Soybean cyst nematode (SCN), Heterodera glycines Ichinohe, is the number 1 pathogen of the important economic crop soybean. Bacteria represent potential biocontrol agents of the SCN, but few studies have characterized the dynamics of bacterial communities associated with cysts under different crop rotation sequences. The bacterial communities in SCN cysts in a long-term soybean–corn crop rotation experiment were investigated over 2 years. The crop sequences included long-term soybean monoculture (Ss), years 1–5 of soybean following 5 years corn (S1–S5), years 1 and 2 of corn following 5 years soybean (C1 and C2), and soybean–corn annual rotation (Sa and Ca). The bacterial 16S rRNA V4 region was amplified from DNA isolated from SCN cysts collected in spring at planting, midseason (2 months later), and fall at harvest and sequenced on the Illumina MiSeq platform. The SCN cyst microbiome was dominated by Proteobacteria followed by Actinobacteria, Bacteroidetes, and Verrucomicrobia. The bacterial community composition was influenced by both crop sequence and season. Although differences by crop sequence were not significant in the spring of each year, bacterial communities in cysts from annual rotation (Sa and Ca) or crop sequences of early years of monoculture following a 5-year rotation of the alternate crop (S1 and C1) became rapidly differentiated by crop over a single growing season. In the fall, genera of cyst bacteria associated with soybean crop sequences included Rhizobacter, Leptothrix, Cytophaga, Chitinophaga, Niastella, Streptomyces, and Halangium. The discovery of diverse bacterial taxa in SCN cysts and their dynamics across crop rotation sequences provides invaluable information for future development of biological control of the SCN.

Faba bean in crop rotation shapes bacterial and fungal communities and nutrient contents under conventional tillage of triticale

Rational cropping maintains high soil fertility and a healthy ecosystem. Soil microorganism is the controller of soil fertility. Meanwhile, soil microbial communities also respond to different cropping patterns. The mechanisms by which biotic and abiotic factors were affected by different cropping sequences remain unclear in the major grain-producing regions of northeastern China. To evaluate the effects of different cropping sequences under conventional fertilization practices on soil properties, microbial communities, and crop yield, six types of plant cropping systems were performed, including soybean monoculture, wheat-soybean rotation, wheat-maize-soybean rotation, soybean-maize-maize rotation, maize-soybean-soybean rotation and maize monoculture. Our results showed that compared with the single cropping system, soybean and maize crop rotation in different combinations or sequences can increase soil total organic carbon and nutrients, and promote soybean and maize yield, especially using soybean-maize-maize and maize-soybean-soybean planting system. The 16S rRNA and internal transcribed spacer (ITS) amplicon sequencing showed that different cropping systems had different effects on bacterial and fungal communities. The bacterial and fungal communities of soybean monoculture were less diverse when compared to the other crop rotation planting system. Among the different cropping sequences, the number of observed bacterial species was greater in soybean-maize-maize planting setup and fungal species in maize-soybean-soybean planting setup. Some dominant and functional bacterial and fungal taxa in the rotation soils were observed. Network-based analysis suggests that bacterial phyla Acidobacteria and Actinobacteria while fungal phylum Ascomycota showed a positive correlation with other microbial communities. The phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) result showed the presence of various metabolic pathways. Besides, the soybean-maize-maize significantly increased the proportion of some beneficial microorganisms in the soil and reduced the soil-borne animal and plant pathogens. These results warrant further investigation into the mechanisms driving responses of beneficial microbial communities and their capacity on improving soil fertility during legume cropping. The present study extends our understanding of how different crop rotations effect soil parameters, microbial diversity, and metabolic functions, and reveals the importance of crop rotation sequences. These findings could be used to guide decision-making from the microbial perspective for annual crop planting and soil management approaches.

Development of a soil quality index for sequences with different levels of land occupation using soil chemical, physical and microbiological properties

Fertilization regime has a greater effect on soil microbial community structure than crop rotation and growth stage in an agroecosystem

Microbes are key components of the soil environment, playing an important role in maintaining soil health, sustainability, and productivity. The composition and structure of soil bacterial communities were examined in winter wheat-rice (WR) and winter wheat-maize (WM) cropping systems derived from five locations in the Low-Middle Yangtze River plain and the Huang-Huai-Hai plain by pyrosequencing of the 16S ribosomal RNA gene amplicons. A total of 102,367 high quality sequences were used for multivariate statistical analysis and to test for correlation between community structure and environmental variables such as crop rotations, soil properties, and locations. The most abundant phyla across all soil samples were Proteobacteria, Acidobacteria, and Bacteroidetes. Similar patterns of bacterial diversity and community structure were observed within the same cropping systems, and a higher relative abundance of anaerobic bacteria was found in WR compared to WM cropping systems. Variance partitioning analysis revealed complex relationships between bacterial community and environmental variables. The effect of crop rotations was low but significant, and interactions among soil properties, locations, and crop rotations accounted for most of the explained variation in the structure of bacterial communities. Soil properties such as pH, available P, and available K showed higher correlations (positive or negative) with the majority of the abundant taxa. Bacterial diversity (the Shannon index) and richness (Chao1 and ACE) were higher under WR than WM cropping systems.

A better understanding of the relationships among different cropping systems, their effects on soil microbial ecology, and their effects on crop health and productivity is necessary for the development of more efficient, sustainable crop production systems. We used denaturing gradient gel electrophoresis (DGGE) to determine the impacts of crop rotations and crop types on bacterial and fungal communities in the soil. The communities of bacterial 16S rRNA genes and fungal 18S rRNA genes were analyzed in experimental field plots that were kept under 4 different crop rotation systems from 1999 to 2008 (continuous cabbage (Brassica oleracea var. capitata L.), cabbage–lettuce (Lactuca sativa L.) rotation, cabbage–radish (Raphanus sativus L. var. longipinnatus L.H. Bailey) rotation, and a 3-year crop rotation). A principal component analysis (PCA) and a canonical correspondence analysis (CCA) revealed that both the bacterial and fungal communities in bulk soils were influenced by the crop rotation systems. However, the primary factors influencing each community differed: bacterial communities were most affected by soil properties (especially carbon content), while fungal communities were influenced most strongly by rotation times. To elucidate factors that may cause differences in crop rhizosphere microbial communities, the microbial communities in the harvested cabbage rhizospheres were also analyzed. The results suggest that the fungal communities in bulk soil are related to the rhizosphere fungal communities. Our present study indicates that the microbial communities in bulk and rhizosphere soils could be managed by crop rotation systems.

Isatis tinctoria L. was cultivated until the 19th century to produce indigo, a natural blue pigment used principally for dyestuffs. The current search for alternative crops and interest in natural products has led to reconsidering I. tinctoria as a crop to be grown in marginal areas to produce natural indigo. To reintroduce I. tinctoria into cultivation, its behaviour under different climatic conditions as well as its morpho-physiological and genetic diversity must be assessed in order to evaluate the possibilities of future breeding work. To do this, a Eurasian collection of 15 accessions was studied in a 2-year experiment. The study was carried out in four locations in order to assess plant performance at altitudes ranging from 380 to 1,700 m a.s.l. A second experiment evaluated the morpho-physiological diversity of several traits (some related to agronomic performances) of the collection. In a third experiment the genetic traits of the collection were characterised by using eight AFLP and eight SAMPL markers. The species showed a wide adaptability to different mountainous conditions and the populations showed high morphologic and genetic variability and differed according to their origins. Both morpho-physiological and molecular characterisation allowed the accessions to be distinguished into groups of European and Asian origin. Future breeding work is recommended because some accessions have good agronomic potential.

The objective of this work was to evaluate the physical quality of an Oxisol under no-tillage subjected to different crop rotations and crop sequences. The experiment was carried out in a clayey Oxisol, during six years, in a randomized complete block design, with strip plots and three replicates. The following physical indicators of soil quality were evaluated: soil density and carbon content, as well as mean weight diameter and tensile strength of aggregates. Treatments consisted of three summer crop rotations - corn/corn (Zea mays), soybean/soybean (Glycine max), and soybean/corn - and of seven second crops (crop sequences) - corn, sunflower (Helianthus annuus), oilseed radish (Raphanus sativus), pearl millet (Pennisetum americanum), pigeon pea (Cajanus cajan), grain sorghum (Sorghum bicolor), and sun hemp (Crotalaria juncea). Crop rotations and sequences did not affect soil carbon contents. Corn, as a summer crop, increased the tensile strength and mean weight diameter of aggregates, similarly to pearl millet and sorghum as second crops. Soybean/corn rotation with sun hemp as a second crop increases soil physical quality, promoting higher tensile strengths and lower soil densities.

Response of potato yield, soil chemical and microbial properties to different rotation sequences of green manure-potato cropping in North China

Agricultural landscape-scale C factor determination and erosion prediction for various crop rotations through a remote sensing and GIS approach

In agricultural systems, soil quality is thought of in terms of productive land that can maintain or increase farm profitability, as well as conserving soil resources so that future farming generations can make a living. Management practices which can modify soil quality include tillage systems and crop rotations. A major proportion of Australian cotton (Gossypium hirsutum L.) is grown on Vertosols (~75%), of which almost 80% is irrigated. These soils have high clay contents (40–80 g/100 g) and strong shrink–swell capacities, but are frequently sodic at depth and prone to deterioration in soil physical quality if incorrectly managed. Due to extensive yield losses caused by widespread deterioration of soil structure and declining fertility associated with tillage, trafficking, and picking under wet conditions during the middle and late 1970s, a major research program was initiated with the objective of developing soil management systems which could improve cotton yields while concurrently ameliorating and maintaining soil structure and fertility. An outcome of this research was the identification of cotton–winter crop sequences sown in a 1 : 1 rotation as being able to sustain lint yields while at the same time maintaining soil physical quality and minimising fertility decline. Consequently, today, a large proportion (~75%) of Australian cotton is grown in rotation with winter cereals such as wheat (Triticum aestivum L.), or legumes such as faba bean (Vicia faba L.). A second phase of research on cotton rotations in Vertosols was initiated during the early 1990s with the main objective of identifying sustainable cotton–rotation crop sequences; viz. crop sequences which maintained and improved soil quality, minimised disease incidence, facilitated soil organic carbon sequestration, and maximised economic returns and cotton water use efficiency in the major commercial cotton-growing regions of Australia. The objective of this review was to summarise the key findings of both these phases of Australian research with respect to soil quality and profitability, and identify future areas of for research. Wheat rotation crops under irrigated and dryland conditions and in a range of climates where cotton is grown can improve soil quality indicators such as subsoil structure, salinity, and sodicity under irrigated and dryland conditions, while leguminous crops can increase available nitrogen by fixing atmospheric nitrogen, and by reducing N volatilisation and leaching losses. Soil organic carbon in most locations has decreased with time, although the rate of decrease may be reduced by sowing crop sequences that return about 2 kg/m2.crop cycle of residues to the soil, minimising tillage and optimising N inputs. Although the beneficial effects of soil biodiversity on quality of soil are claimed to be many, except for a few studies on soil macrofauna such as ants, conclusive field-based evidence to demonstrate this has not been forthcoming with respect to cotton rotations. In general, lowest average lint yields per hectare were with cotton monoculture. The cotton–wheat systems generally returned higher average gross margins/ML irrigation water than cotton monoculture and other rotation crops. This indicates that where irrigation water, rather than land, is the limiting resource, cotton–wheat systems would be more profitable. Recently, the addition of vetch (Vicia villosa Roth.) to the cotton–wheat system has further improved average cotton yields and profitability. Profitability of cotton–wheat sequences varies with the relative price of cotton to wheat. In comparison with cotton monoculture, cotton–rotation crop sequences may be more resilient to price increases in fuel and fertiliser due to lower overall input costs. The profitability of cotton–rotation crop sequences such as cotton–wheat, where cotton is not sown in the same field every year, is more resilient to fluctuations in the price of cotton lint, fuel and nitrogen fertiliser. This review identified several issues with respect to cotton–rotation crop sequences where knowledge is lacking or very limited. These are: research into ‘new’ crop rotations; comparative soil quality effects of managing rotation crop stubble; machinery attachments for managing rotation crop stubble in situ in permanent bed systems; the minimum amount of crop stubble which needs to be returned per cropping cycle to increase SOC levels from present values; the relative efficacy of C3 and C4 rotation crops in relation to carbon sequestration; the interactions between soil biodiversity and soil physical and chemical quality indicators, and cotton yields; and the effects of sowing rotation crops after cotton on farm and cotton industry economic indicators such as the economic incentives for adopting new cotton rotations, farm level impacts of research and extension investments, and industry- and community/catchment-wide economic modelling of the impact of cotton research and extension activities.

Composition, predicted functions, and co-occurrence networks of fungal and bacterial communities_ Links to soil organic carbon under long-term fertilization in a rice-wheat cropping system

BackgroundCrop rotation is an agronomic practice that is known to enhance productivity and yield, and decrease pest and disease pressure. Economic and other factors have increased the frequency of certain crops, including canola, with unknown effects on the below ground microbial communities that impact plant health and performance. This study investigated the effect of 12 years of crop rotation including canola-wheat; canola-pea-barley; and unrotated canola across three geographic sites in Western Canada with diverse soil types and environmental conditions. To provide data on mature, established crop rotation strategies, root exudate profiles, soil nutrient fluxes, and bacterial and fungal microbial community profiles were determined at the flowering stage in the final two (canola) years of the 12-year rotations.ResultsAfter 12 years of rotation, nutrient fluxes were affected in the soil in an inconsistent manner, with K, NO3, Mg, Ca, P, and Fe fluxes variably impacted by rotation depending on the year and site of sampling. As expected, rotation positively influenced yield and oil content, and decreased disease pressure from Leptosphaeria and Alternaria. In two of the three sites, root exudate profiles were significantly influenced by crop rotation. Bacterial soil, root, and rhizosphere communities were less impacted by crop rotation than the fungal communities. Fungal sequences that were associated with specific rotation strategies were identified in the bulk soil, and included known fungal pathogens in the canola-only strategy. Two closely related fungal sequences identified as Olpidium brassicae were extremely abundant at all sites in both years. One of these sequences was observed uniquely at a single site and was significantly associated with monocropped canola; moreover, its abundance correlated negatively with yield in both years.ConclusionsLong-term canola monoculture affected root exudate profiles and soil nutrient fluxes differently in the three geographic locations. Bacterial communities were less impacted by rotation compared to the fungal communities, which consistently exhibited changes in composition in all ecological niches at all sites, in both years. Fungal sequences identified as O. brassicae were highly abundant at all sites, one of which was strongly associated with canola monoculture. Soil management decisions should include consideration of the effects on the microbial ecosystems associated with the plants in order to inform best management practices.

Crop rotations alter bacterial and fungal diversity in paddy soils across East Asia