Effect of Long-Term Agricultural Management on the Soil Microbiota Influenced by the Time of Soil Sampling

Application of agrochemicals and mechanization enabled increasing agriculturalproductivity yet caused various environmental and soil health-related problems.Agricultural practices affect soil microorganisms, which are the key players of manyecosystem processes. However, less is known about whether this effect differs betweentime points. Therefore, soil was sampled in winter (without crop) and in summer (inthe presence of maize) from a long-term field experiment (LTE) in Bernburg (Germany)managed either under cultivator tillage (CT) or moldboard plow (MP) in combinationwith either intensive nitrogen (N)-fertilization and pesticides (Int) or extensive reducedN-fertilization without fungicides (Ext), respectively. High-throughput sequencing of 16SrRNA gene and fungal ITS2 amplicons showed that changes in the microbial communitycomposition were correlated to differences in soil chemical properties caused by tillagepractice. Microbial communities of soils sampled in winter differed only depending onthe tillage practice while, in summer, also a strong effect of the fertilization intensity wasobserved. A small proportion of microbial taxa was shared between soils from the twosampling times, suggesting the existence of a stable core microbiota at the LTE. Ingeneral, taxa associated with organic matter decomposition (such as Actinobacteria,Bacteroidetes, Rhizopus, and Exophiala) had a higher relative abundance under CT.Among the taxa with significant changes in relative abundances due to different long-termagricultural practices were putative pathogenic (e.g., Gibellulopsis and Gibberella) andbeneficial microbial genera (e.g., Chitinophagaceae, Ferruginibacter, and Minimedusa).In summary, this study suggests that the effects of long-term agricultural managementpractices on the soil microbiota are influenced by the soil sampling time, and this needsto be kept in mind in future studies for the interpretation of field data.Fil: Fernandez Gnecco, Gabriela Amancay. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones en Biodiversidad y Biotecnología; ArgentinaFil: Covacevich, Fernanda. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones en Biodiversidad y Biotecnología; ArgentinaFil: Consolo, Verónica Fabiana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones en Biodiversidad y Biotecnología; ArgentinaFil: Behr, Jan H.. Leibniz Institute Of Vegetable And Ornamental Crops (; AlemaniaFil: Sommermann, Loreen. Department Of Agriculture, Ecotrophology And Landscape; AlemaniaFil: Moradtalab, Narges. Department Of Nutritional Crop Physiology, Institute Of; AlemaniaFil: Maccario, Lorrie. Section Of Microbiology, Department Of Biology, Univers; AlemaniaFil: Sørensen, Søren J.. Section Of Microbiology, Department Of Biology, Univers; AlemaniaFil: Deubel, Annette. Department Of Agriculture, Ecotrophology And Landscape; AlemaniaFil: Schellenberg, Ingo. Department Of Agriculture, Ecotrophology And Landscape; AlemaniaFil: Geistlinger, Joerg. Department Of Agriculture, Ecotrophology And Landscape; AlemaniaFil: Neumann, Günter. Department Of Nutritional Crop Physiology, Institute Of; AlemaniaFil: Grosch, Rita. Leibniz Institute Of Vegetable And Ornamental Crops (; AlemaniaFil: Smalla, Kornelia. Julius Kühn Institut Braunschweig; AlemaniaFil: Babin, Doreen. Julius Kühn Institut Braunschweig; Alemani

The relationships between West Nile and Kunjin viruses.

Until recently, West Nile (WN) and Kunjin (KUN) viruses were classified as distinct types in the Flavivirus genus. However, genetic and antigenic studies on isolates of these two viruses indicate that the relationship between them is more complex. To better define this relationship, we performed sequence analyses on 32 isolates of KUN virus and 28 isolates of WN virus from different geographic areas, including a WN isolate from the recent outbreak in New York. Sequence comparisons showed that the KUN virus isolates from Australia were tightly grouped but that the WN virus isolates exhibited substantial divergence and could be differentiated into four distinct groups. KUN virus isolates from Australia were antigenically homologous and distinct from the WN isolates and a Malaysian KUN virus. Our results suggest that KUN and WN viruses comprise a group of closely related viruses that can be differentiated into subgroups on the basis of genetic and antigenic analyses

Impact of long-term agricultural management practices on soil prokaryotic communities

International audienceThe profound intensification of agricultural practices by increased application of agro-chemicals, short crop rotations and ploughing resulted in loss of soil fertility, erosion and accumulation of soil-borne plant pathogens. Soil microbial communities are key players in ecosystem processes and are intimately linked to crop productivity and health. Thus a better understanding of how farming practices affect soil microbiota is needed in order to promote sustainable agriculture. The long-term field trial in Bernburg (Germany) established in 1992 provides a unique opportunity to assess the effects of i) the crop (maize vs. rapeseed) preceding the actual winter wheat culture, ii) tillage practice (mouldboard plough vs. cultivator tillage) and iii) standard nitrogen (N)-fertilization intensity with application of growth regulators and fungicides (intensive) compared to reduced N-fertilization without growth regulators and fungicides (extensive). We hypothesized that these different farming practices affect the soil prokaryotic community structures with consequences for their functional potential. Total community-DNA was extracted directly from soils sampled at wheat harvest. Illumina sequencing of 16S rRNA genes amplified from total community-DNA revealed a significant effect of tillage practice and the preceding crop on prokaryotic community structures, whereas the influence of N-fertilization intensity was marginal. A number of differentially abundant prokaryotic genera and their predicted functions between mouldboard plough vs. cultivator tillage as well as between different preceding crops were identified. Compared to extensive N-fertilization, intensive N-fertilization resulted in higher abundances of bacterial but not of archaeal amoA genes, that are involved in ammonia oxidation. Our data suggest that long-term farming strategies differently shape the soil prokaryotic community structure and functions, which should be considered when evaluating agricultural management strategies regarding their sustainability, soil health and crop performance

Organic farming systems affect carbon stocks but not soil structure and associated physical properties in a long-term farming trial on Chernozem

An asset of organic farming systems with diversified crop rotations, next to a cut in pesticide and mineral fertilizer application, is the built-up of organic carbon stocks in the long-term. In addition, the inclusion of deep-rooting legumes like alfalfa is known to improve soil structure and increase particulate organic matter contents in the subsoil. These views have been challenged recently ascribing limited potential for legume-based crop rotations to increase carbon stocks in Chernozems (Mollisols) due to limited accrual of mineral-associated organic carbon. Likewise, the direct impact of these legumes on soil structure and associated soil properties like water retention and transport has been questioned and linked to indirect effects instead. The objective of this study was to investigate the impact of legume-based crop rotations on carbon stocks and soil structure properties in the Flurweg II long-term farming systems trial (26 years) established on a Chernozem soil in Germany. We compared one conventional (INT) and two organic farming systems, with (O + M) and without (O - M) integrated livestock management. The three farming systems differ in biomass return via plant residues or farmyard manure as well as share and type of legumes in the eight-year crop rotation (INT: pea, O - M: faba bean and pea, O + M: biannual alfalfa). The comparison included yields, carbon stocks, soil physical properties and microstructure properties based on X-ray computed tomography of soil within and beneath the plow horizon. All farming systems underwent conventional plowing. In addition, we compared carbon stocks and microstructure properties with those from the nearby Westerfeld tillage trial with conventional and reduced tillage in a legume-free crop rotation. The carbon stocks in the plowed topsoil of the Flurweg II systems trial increased significantly with organic farming including livestock (INT: 53 ± 2 vs. O + M: 61 ± 2 t ha−1), but not without (O - M: 53 ± 4 t ha−1), likely because of farmyard manure application in the O + M system. This increase in topsoil carbon stocks is only moderate compared to the increase in topsoil carbon stocks in the Westerfeld tillage trial by switching from conventional to reduced tillage (53 vs. 70 t ha−1). The carbon stocks of the whole soil profile (down to 48 cm) in the Flurweg II systems trial tended to increase with organic farming irrespective of livestock integration (INT: 72 ± 5 t ha−1 vs. O ± M: 82–83 ± 7 t ha−1). Particulate organic matter (POM) contents and biopore diameter below the plow layer tended to increase with alfalfa in the crop rotation of the O + M farming system. However, the legacy effect four years after the presence or absence of alfalfa was only in the range of natural, spatial variability. As a result of similar soil microstructure there was also hardly any difference in hydraulic conductivity and no difference in soil mechanical properties between farming systems. This study shows that Chernozems in this region still have the capacity to increase POM contents and carbon stocks with climate-smart, regenerative agricultural management, but also demonstrate that this has limited effects on structural properties

Organic farming systems affect carbon stocks but not soil structure and associated physical properties in a long-term farming trial on Chernozem

An asset of organic farming systems with diversified crop rotations, next to a cut in pesticide and mineral fertilizer application, is the built-up of organic carbon stocks in the long-term. In addition, the inclusion of deep-rooting legumes like alfalfa is known to improve soil structure and increase particulate organic matter contents in the subsoil. These views have been challenged recently ascribing limited potential for legume-based crop rotations to increase carbon stocks in Chernozems (Mollisols) due to limited accrual of mineral-associated organic carbon. Likewise, the direct impact of these legumes on soil structure and associated soil properties like water retention and transport has been questioned and linked to indirect effects instead.The objective of this study was to investigate the impact of legume-based crop rotations on carbon stocks and soil structure properties in the Flurweg II long-term farming systems trial (26 years) established on a Chernozem soil in Germany. We compared one conventional (INT) and two organic farming systems, with (O + M) and without (O - M) integrated livestock management. The three farming systems differ in biomass return via plant residues or farmyard manure as well as share and type of legumes in the eight-year crop rotation (INT: pea, O - M: faba bean and pea, O + M: biannual alfalfa). The comparison included yields, carbon stocks, soil physical properties and microstructure properties based on X-ray computed tomography of soil within and beneath the plow horizon. All farming systems underwent conventional plowing. In addition, we compared carbon stocks and microstructure properties with those from the nearby Westerfeld tillage trial with conventional and reduced tillage in a legume-free crop rotation.The carbon stocks in the plowed topsoil of the Flurweg II systems trial increased significantly with organic farming including livestock (INT: 53 ± 2 vs. O + M: 61 ± 2 t ha−1), but not without (O - M: 53 ± 4 t ha−1), likely because of farmyard manure application in the O + M system. This increase in topsoil carbon stocks is only moderate compared to the increase in topsoil carbon stocks in the Westerfeld tillage trial by switching from conventional to reduced tillage (53 vs. 70 t ha−1). The carbon stocks of the whole soil profile (down to 48 cm) in the Flurweg II systems trial tended to increase with organic farming irrespective of livestock integration (INT: 72 ± 5 t ha−1 vs. O ± M: 82–83 ± 7 t ha−1). Particulate organic matter (POM) contents and biopore diameter below the plow layer tended to increase with alfalfa in the crop rotation of the O + M farming system. However, the legacy effect four years after the presence or absence of alfalfa was only in the range of natural, spatial variability. As a result of similar soil microstructure there was also hardly any difference in hydraulic conductivity and no difference in soil mechanical properties between farming systems.This study shows that Chernozems in this region still have the capacity to increase POM contents and carbon stocks with climate-smart, regenerative agricultural management, but also demonstrate that this has limited effects on structural properties

Redox homeostasis and cell cycle activation mediate beta-cell mass expansion in aged, diabetes-prone mice under metabolic stress conditions: Role of thioredoxin-interacting protein (TXNIP)

Overnutrition contributes to insulin resistance, obesity and metabolic stress, initiating a loss of functional beta-cells and diabetes development. Whether these damaging effects are amplified in advanced age is barely investigated. Therefore, New Zealand Obese (NZO) mice, a well-established model for the investigation of human obesity-associated type 2 diabetes, were fed a metabolically challenging diet with a high-fat, carbohydrate restricted period followed by a carbohydrate intervention in young as well as advanced age. Interestingly, while young NZO mice developed massive hyperglycemia in response to carbohydrate feeding, leading to beta-cell dysfunction and cell death, aged counterparts compensated the increased insulin demand by persistent beta-cell function and beta-cell mass expansion. Beta-cell loss in young NZO islets was linked to increased expression of thioredoxin-interacting protein (TXNIP), presumably initiating an apoptosis-signaling cascade via caspase-3 activation. In contrast, islets of aged NZOs exhibited a sustained redox balance without changes in TXNIP expression, associated with higher proliferative potential by cell cycle activation. These findings support the relevance of a maintained proliferative potential and redox homeostasis for preserving islet functionality under metabolic stress, with the peculiarity that this adaptive response emerged with advanced age in diabetes-prone NZO mice

Identification of biomarkers of brown adipose tissue aging highlights the role of dysfunctional energy and nucleotide metabolism pathways

Brown adipose tissue function declines during aging and may contribute to the onset of metabolic disorders such as diabetes and obesity. Only limited understanding of the mechanisms leading to the metabolic impairment of brown adipocytes during aging exists. To this end, interscapular brown adipose tissue samples were collected from young and aged mice for quantification of differential gene expression and metabolite levels. To identify potential processes involved in brown adipocyte dysfunction, metabolite concentrations were correlated to aging and significantly changed candidates were subsequently integrated with a non-targeted proteomic dataset and gene expression analyses. Our results include novel age-dependent correlations of polar intermediates in brown adipose tissue. Identified metabolites clustered around three biochemical processes, specifically energy metabolism, nucleotide metabolism and vitamin metabolism. One mechanism of brown adipose tissue dysfunction may be linked to mast cell activity, and we identify increased histamine levels in aged brown fat as a potential biomarker. In addition, alterations of genes involved in synthesis and degradation of many metabolites were mainly observed in the mature brown adipocyte fraction as opposed to the stromal vascular fraction. These findings may provide novel insights on the molecular mechanisms contributing to the impaired thermogenesis of brown adipocytes during aging