Microbial transfers from permanent grassland ecosystems to milk in dairy farms in the Comté cheese area

Microbial composition and viability of natural whey starters used in PDO Comté cheese-making

Natural whey starters (NWS) are cultures with undefined multiple-strains species commonly used to speed up the fermentation process of cheeses. The aim of this study was to explore the diversity and the viability of Comté cheese NWS microbiota. Culture-dependent methods, i.e. plate counting and genotypic characterization, and culture-independent methods, i.e. qPCR, viability-qPCR, fluorescence microscopy and DNA metabarcoding, were combined to analyze thirty-six NWS collected in six Comté cheese factories at two seasons. Our results highlighted that NWS were dominated by Streptococcus thermophilus (ST) and thermophilic lactobacilli. These species showed a diversity of strains based on Rep-PCR. The dominance of Lactobacillus helveticus (LH) over Lactobacillus delbrueckii (LD) varied depending on the factory and the season. This highlighted two types of NWS: the type-ST/LD (LD > LH) and the type-ST/LH (LD < LH). The microbial composition varied depending on cheese factory. One factory was distinguished by its level of culturable microbial groups (ST, enterococci and yeast) and its fungi diversity. The approaches used to estimate the viability showed that most NWS cells were viable. Further investigations are needed to understand the microbial diversity of these NWS.

Dietary Live Yeast Supplementation Influence on Cow’s Milk, Teat and Bedding Microbiota in a Grass-Diet Dairy System

The supplementation of animal feed with microbial additives remains questioning for the traditional or quality label raw milk cheeses with regard to microbial transfer to milk. We evaluated the effect of dietary administration of live yeast on performance and microbiota of raw milk, teat skin, and bedding material of dairy cows. Two balanced groups of cows (21 primiparous 114 ± 24 DIM, 18 multiparous 115 ± 33 DIM) received either a concentrate supplemented with Saccharomyces cerevisiae CNCM I-1077 (1 × 1010 CFU/d) during four months (LY group) or no live yeast (C group). The microbiota in individual milk samples, teat skins, and bedding material were analysed using culture dependent techniques and high-throughput amplicon sequencing. The live yeast supplementation showed a numerical increase on body weight over the experiment and there was a tendency for higher milk yield for LY group. A sequence with 100% identity to that of the live yeast was sporadically found in fungal amplicon datasets of teat skin and bedding material but never detected in milk samples. The bedding material and teat skin from LY group presented a higher abundance of Pichia kudriavzevii reaching 53% (p < 0.05) and 10% (p < 0.05) respectively. A significant proportion of bacterial and fungal ASVs shared between the teat skin and the milk of the corresponding individual was highlighted.

Dynamic of bacterial and archaeal diversity in a tropical soil over 6 years of repeated organic and inorganic fertilization

The soil microbial community plays important roles in nutrient cycling, plant pathogen suppression, decomposition of residues and degradation of pollutants; as such, it is often regarded as a good indicator of soil quality. Repeated applications of mixed organic and inorganic materials in agriculture improve the soil microbial quality and in turn crop productivity. The soil microbial quality following several years of repeated fertilizer inputs has received considerable attention, but the dynamic of this community over time has never been assessed. We used high-throughput sequencing targeting 16S ribosomal RNA genes to investigate the evolution of the bacterial and archaeal community throughout 6 years of repeated organic and inorganic fertilizer applications. Soils were sampled from a field experiment in La Mare (Reunion Island, France), where different mixed organic-inorganic fertilizer inputs characterized by more or less stable organic matter were applied regularly for 6 years. Soil samples were taken each year, more than 6 months after the latest fertilizer application. The soil molecular biomass significantly increased in some organically fertilized plots (by 35–45% on average), 3–5 years after the first fertilizers application. The significant variations in soil molecular microbial biomass were explained by the fertilization practices (cumulated organic carbon inputs) and sometimes by the soil parameters (sand and soil carbon contents). The structure of the bacterial and archaeal community was more influenced by time than by the fertilization type. However, repeated fertilizer applications over time tended to modify the abundance of the bacterial phyla Acidobacteria, Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria. To conclude, the present study highlights that the soil bacterial and archaeal community is lastingly modified after 6 years of repeated fertilizer inputs. These changes depend on the nature of the organic input and on the fertilization practice (frequency and applied quantity).

Effect of Straw and Wood Ash on Soil Carbon Sequestration and Bacterial Community in a Calcareous Soil

Soil fertility can be improved by effectively utilizing agricultural waste. Straw can supply energy and wood ash adds nutrients to improve soil quality. However, few kinds of research have investigated the effect of wood ash and straw on soil carbon sequestration and the soil bacterial population, particularly in calcareous soils. The main goal of this current study was to quantify the impact of a combination of wood ash and straw on the indicators described above using stable δ13C isotope analyses by applying wheat straw to calcareous soil under a long-term C4 crop rotation. The incubation experiment included four treatments as follows: (i) no amendment (Control); (ii) amendment with wood ash (W); (iii) amendment with straw (S); and (iv) a combined amendment of straw and wood ash (SW). Our results showed that sequestration of soil inorganic carbon (SIC) in the SW and W treatments was higher (an average of 7.78%) than that in the S and Control treatments. The sequestered soil organic carbon (SOC) in the SW treatment was 1.25-fold greater than that in the S treatment, while there was no evident effect on the SOC content compared with straw alone. The microbial biomass carbon increased under SW by 143.33%, S by 102.23%, and W by 13.89% relative to control. The dissolved organic carbon increased under SW by 112.0%, S by 66.61%, and W by 37.33% relative to the control. The pH and electrical conductivity were higher in the SW and W treatments than in the S treatment and the control. The SW was conducive to maintaining soil enzymatic activities and bacterial diversity. Bacteroidetes and Actinobacteriota were dominant in SW, while the Acidobacteria phyla were dominant in the S treatment. The diversity of bacteria in the soil and community composition of the bacteria were predominantly assessed by the levels of water-soluble K, pH, and electrical conductivity. The incorporation of straw and wood ash is probably more effective at improving SIC and SOC sequestration and ameliorates the soil microhabitat.

Potential of Meta-Omics to Provide Modern Microbial Indicators for Monitoring Soil Quality and Securing Food Production

Soils are fundamental resources for agricultural production and play an essential role in food security. They represent the keystone of the food value chain because they harbor a large fraction of biodiversity—the backbone of the regulation of ecosystem services and “soil health” maintenance. In the face of the numerous causes of soil degradation such as unsustainable soil management practices, pollution, waste disposal, or the increasing number of extreme weather events, it has become clear that (i) preserving the soil biodiversity is key to food security, and (ii) biodiversity-based solutions for environmental monitoring have to be developed. Within the soil biodiversity reservoir, microbial diversity including Archaea, Bacteria, Fungi and protists is essential for ecosystem functioning and resilience. Microbial communities are also sensitive to various environmental drivers and to management practices; as a result, they are ideal candidates for monitoring soil quality assessment. The emergence of meta-omics approaches based on recent advances in high-throughput sequencing and bioinformatics has remarkably improved our ability to characterize microbial diversity and its potential functions. This revolution has substantially filled the knowledge gap about soil microbial diversity regulation and ecology, but also provided new and robust indicators of agricultural soil quality. We reviewed how meta-omics approaches replaced traditional methods and allowed developing modern microbial indicators of the soil biological quality. Each meta-omics approach is described in its general principles, methodologies, specificities, strengths and drawbacks, and illustrated with concrete applications for soil monitoring. The development of metabarcoding approaches in the last 20 years has led to a collection of microbial indicators that are now operational and available for the farming sector. Our review shows that despite the recent huge advances, some meta-omics approaches (e.g., metatranscriptomics or meta-proteomics) still need developments to be operational for environmental bio-monitoring. As regards prospects, we outline the importance of building up repositories of soil quality indicators. These are essential for objective and robust diagnosis, to help actors and stakeholders improve soil management, with a view to or to contribute to combining the food and environmental quality of next-generation farming systems in the context of the agroecological transition.

Effects of Temperature and Nitrogen Application on Carbon and Nitrogen Accumulation and Bacterial Community Composition in Apple Rhizosphere Soil

Malus sieversii grows on the slopes of the Tianshan Mountains in Xinjiang where the difference in daily temperature is significant. In recent years, the rhizosphere soil health of Malus sieversii has been severely impacted by anthropogenic disturbance and pathogenic infestation. The soil nutrient content and soil microorganism diversity are the main components of soil health. Low temperature has negative effects on soil bacterial community structure by inhibiting the accumulation of carbon and nitrogen. However, the effects of temperature and nitrogen application on soil carbon and nitrogen accumulation and the bacterial community composition in the rhizosphere soil of Malus sieversii are unclear. We set two temperature levels, i.e., low temperature (L) and room temperature (R), combined with no nitrogen (N0) and nitrogen application (N1) to explore the response of plant carbon and nitrogen uptake, rhizosphere soil carbon and nitrogen accumulation and bacterial community composition to temperature and nitrogen fertilization. At the same temperature level, plant 13C abundance (P-Atom13C), plant 15N absolute abundance (P-Con15N), soil 15N abundance (S-Atom15N) and soil urease, protease and glutaminase activities were significantly higher under nitrogen application compared with the no-nitrogen application treatment. The bacterial community diversity and richness indices of the apple rhizosphere soil in the N1 treatment were higher than those in the N0 treatment. The relative abundances of Actinobacteria, Rhodopseudomonas, and Bradyrhizobium were higher in the LN1 treatment than in the LN0 treatment. Redundancy analysis (RDA) showed that plant 13C absolute abundance (P-Con13C) and plant 15N absolute abundance (P-Con15N) were the main factors affecting the soil bacterial community composition. In summary, Nitrogen application can alleviate the effects of low temperature stress on the soil bacterial community and is of benefit for the uptakes of carbon and nitrogen in Malus sieversii plants.