Core Bacterial Community Research Articles

Analysis of Bacterial Community Composition and Ecological Function during Soft Rot Process in Pitaya (Hylocereus spp.) Stems

The soft rot in pitaya (Hylocereus spp.) stems seriously affected the harvest of pitaya fruits, but the dynamic change characteristics of bacterial community in pitaya stems during soft rot stages had not been revealed. In this study, we analyzed the bacterial community composition of different soft rot stages and visualized functional annotations of the core bacterial community in five soft rot periods via the Illumina high-throughput sequencing technology, MetaCoMET online network platform, and FAPROTAX database. The results showed that the dominant bacteria in healthy and diseased pitaya stems were Proteobacteria and Firmicutes. Pseudomonas, Enterobacter, Sphingomonas, and Sphingobacterium were the core bacteria microbiomes during the infection stages. Meanwhile, the ecological function analysis results showed that the Enterobacter and Pseudomonas bacteria may play an important role in causing soft rot of pitaya stems. Therefore, the results shown in this paper could provide a useful reference for the study on microecological mechanism of soft rot of pitaya stems.

Developmental microbiome of the small carpenter bee, Ceratina calcarata

AbstractThe importance of the holobiont has been studied across many bee species, but less is known about the changes in the microbiome throughout the course of development, particularly in subsocial bees. This study used 16S rRNA and ITS amplicon sequencing of pollen provisions and individuals of the small carpenter bee, Ceratina calcarata, across stages of development to characterize the composition and diversity of bacteria and fungi in the microbiome. Pollen provisions and larval stages showed similar beta diversity, but differences in taxa composition. There was no significant decrease in diversity during the transition between larval and pupal stages that was expected post defecation. However, there were unexpected and progressive declines in diversity as development progressed from the early to late pupal stages and again from the callow to adult stages. Bees across all stages lacked members of the Lactobacillus (now Apilactobacillus) genus, which has been shown in other studies to be part of the core bacterial community in C. calcarata and all bees. Three correlations between bacteria and fungi were found, suggesting common beneficial bacteria may protect the bees from prevalent fungal pathogens. Low alpha diversity, particularly in the later stages of development through adulthood, is concerning as the microbiome plays an important role in maintaining wild bee health.

The active role of metabolic regulators in nitrogen loss reduction and organic nitrogen transformation during different materials composting

The tricarboxylic acid cycle experienced will cause a lot of carbon and nitrogen (N) losses during aerobic composting, and the greenhouse gases produced will do great harm to ecological balance and human health. Thus, the purpose of this study was to investigate the role of metabolic regulators like adenosine triphosphate and malonic acid in the organic N transformation and N loss reduction in the composting of chicken manure (CM) and garden waste (GW). Results showed that the addition of metabolic regulators promoted organic N transformation and significantly increased organic N content during composting. Concurrently, adding metabolic regulators reduced N loss, especially in GWATP and GWMA compost, the N loss reduced by 27.99% and 29.10%, respectively. However, metabolic regulators played different roles due to different basic properties of materials. The amino acid N, amino sugar N and hydrolysable unknown N (HUN) were stored in GW, while only amide N and HUN were stored in CM. Moreover, adding metabolic regulators significantly increased the core bacterial community associated with organic N transformation. Ultimately, structural equation model and variance partitioning analysis proved that adding metabolic regulators strengthened the effects of environmental factors and bacterial communities on the transformation and content of organic N. Therefore, adding metabolic regulators had positive effect on promoting N cycle.

Identifying the role of fired clay minerals on reducing of nitrogen loss and immobilization of organic nitrogen during chicken manure composting

This study compared effects of clay minerals before and after firing in immobilization of organic nitrogen and reducing of nitrogen loss during chicken manure composting. The clay minerals and fired clay minerals treatments increased organic nitrogen contents and significantly reduced nitrogen loss, the loss was in order CK (52.61%) > M (47.15%) > I (45.90%) > M- (42.58%) > I- (40.59%). Meanwhile, network analysis indicated that core bacterial community associated with nitrogen transformation were more abundant, and conversion effect of single core bacteria on nitrogen components was enhanced in fired clay minerals treatments. In addition, fired clay minerals strengthened correlation between environmental factors, bacterial community and organic nitrogen, and enhanced interaction of abiotic and biotic pathways, which verified by variance partitioning analysis and structural equation model. Therefore, fired clay minerals play a remarkable driving role in formation and immobilization of organic nitrogen.

Site and land-use associations of soil bacteria and fungi define core and indicative taxa.

ABSTRACTSoil microbial diversity has major influences on ecosystem functions and services. However, due to its complexity and uneven distribution of abundant and rare taxa, quantification of soil microbial diversity remains challenging and thereby impeding its integration into long-term monitoring programs. Using metabarcoding, we analyzed soil bacterial and fungal communities at 30 long-term soil monitoring sites from the three land-use types arable land, permanent grassland, and forest with a yearly sampling between snowmelt and first fertilization over five years. Unlike soil microbial biomass and alpha-diversity, microbial community compositions and structures were site- and land-use-specific with CAP reclassification success rates of 100%. The temporally stable site core communities included 38.5% of bacterial and 33.1% of fungal OTUs covering 95.9% and 93.2% of relative abundances. We characterized bacterial and fungal core communities and their land-use associations at the family-level. In general, fungal families revealed stronger land-use associations as compared to bacteria. This is likely due to a stronger vegetation effect on fungal core taxa, while bacterial core taxa were stronger related to soil properties. The assessment of core communities can be used to form cultivation-independent reference lists of microbial taxa, which may facilitate the development of microbial indicators for soil quality and the use of soil microbiota for long-term soil biomonitoring.

Regional discrepancy of microbial community structure in activated sludge system from Chinese WWTPs based on high-throughput 16S rDNA sequencing

Overall understanding of microbial community structure in activated sludge (AS) system at regional level is of great significance for operation regulation of wastewater treatment plants (WWTPs). In this study, 110 AS samples from 21 cities in different Chinese regions were analyzed based on high-throughput 16S ribosomal DNA (rDNA) sequencing to explore effects of different regions on microbial community structure. Results showed that the regions with different characteristics (south and north, coastal and inland, high GDP and low GDP) had great impact on AS bacterial community in China. Core bacterial communities (101 OTUs) in south China were more abundant than those in north China (49 OTUs), and many core species in south China were associated with nutrient removal. Coastal WWTPs possessed unique bacterial communities due to the influence of marine bacteria. Phyla Chloroflexi and Acidobacteria were observed to be main biomarkers in coastal WWTPs. Compared with low GDP regions, more diverse microbial community and effective wastewater treatment were discovered in high GDP regions, and environmental factor analysis suggested that they were mainly correlated with high capacity and influent TP in the WWTPs. β nearest taxon index (βNTI) analysis showed that microbial community assembly in the analyzed AS samples was dominated by deterministic factors (70.67%) and influent quality was observed to be main factor.

Impact of inoculation and turning for full-scale composting on core bacterial community and their co-occurrence compared by network analysis

Window composting with inoculation or frequent turning is a superior way to improve traditional composting efficiency. However, the relationship between the innocent treatment in composting with inoculation or turning and microbial dynamics is unclear. Here, the impact of inoculation and turning for full scale composting on core bacterial community and their co-occurrence network as well as harmless level were compared by network analysis. Results showed that composts with both inoculation and turning had 46% increase of total organic carbon degradation compared to traditional composting and decreased the abundance of potential pathogens. The relative abundance of thermophilic bacteria and Galbibacter, Methylocaldum, Steroidobacter, etc. increased during composting with turning and inoculation. Luteimonas, Sphaerobacter, Turicibacter and Flavobacterium as core bacteria had significant difference between control and composting with enhanced innocent treatment efficiency. Network analysis suggested that turning increased the number of indigenous core bacteria and inoculation enhanced the interaction among key bacterial network.

Characterization of microbial communities from rumen and large intestine of lactating creole goats grazing in arid plant communities.

Arid plant communities provide variable diets that can affect digestive microbial communities of free-foraging ruminants. Thus, we used next-generation sequencing of 16S and 18S rDNA to characterize microbial communities in the rumen (regurgitated digesta) and large intestine (faeces) and diet composition of lactating creole goats from five flocks grazing in native plant communities in the Sonoran Desert in the rainy season. The bacterial communities in the rumen and large intestine of the five flocks had similar alpha diversity (Chao1, Shannon, and Simpson indices). However, bacterial community compositions were different: a bacterial community dominated by Proteobacteria in the rumen transitioned to a community dominated by Firmicutes in the large intestine. Bacterial communities of rumen were similar across flocks; similarly occurred with large-intestine communities. Archaea had a minimum presence in the goat digestive tract. We detected phylum Basidiomycota, Ascomycota, and Apicomplexa as the main fungi and protozoa. Analyses suggested different diet compositions; forbs and grasses composed the bulk of plants in the rumen and forbs and shrubs in faeces. Therefore, lactating goats consuming different diets in the Sonoran Desert in the rainy season share a similar core bacterial community in the rumen and another in the large intestine and present low archaeal communities.

Bacterial community succession and biogenic amine changes during fermentation of fish‐chili paste inoculated with different commercial starter cultures

SummaryThe microbial dynamics, diversity and succession characterisation during the fermentation of fish‐chili paste, with and without starter cultures by high‐throughput sequencing, were investigated to identify the relationship between microbial composition and the accumulation of biogenic amines. Results showed that Firmicutes was the predominant phylum, and Lactobacillus and Weissella were the main genera during fermentation process, regardless of the inclusion of starter cultures. Compared with naturally fermented samples (NS; no starter cultures), Pediococcus and Staphylococcus flourished in samples inoculated with SBM‐52 starter culture (Staphylococcus xylosus + Staphylococcus carnosus + Pediococcus pentosaceus + Pediococcus acidilactici). Staphylococcus also accounted for a larger proportion in samples inoculated with WBX‐43 starter culture (Staphylococcus xylosus + Staphylococcus carnosus). Furthermore, Enterobacter was inhibited in inoculated samples. Unweighted pair‐group method with arithmetic means and principal component analyses revealed that microbiota structures were different among NS, SBM and WBX samples. In case of biogenic amines, the concentration of putrescine, cadaverine and tyramine increased to higher levels in NS samples compared with inoculated samples. Our work also investigated the relationship between core bacterial communities and biogenic amines. This study provided an improved understanding for the effects of starter cultures on the microbial community and the quality of fish‐chili paste.

Biogeography rather than substrate type determines bacterial colonization dynamics of marine plastics.

Since the middle of the 20th century, plastics have been incorporated into our everyday lives at an exponential rate. In recent years, the negative impacts of plastics, especially as environmental pollutants, have become evident. Marine plastic debris represents a relatively new and increasingly abundant substrate for colonization by microbial organisms, although the full functional potential of these organisms is yet to be uncovered. In the present study, we investigated plastic type and incubation location as drivers of marine bacterial community structure development on plastics, i.e., the Plastisphere, via 16S rRNA amplicon analysis. Four distinct plastic types: high-density polyethylene (HDPE), linear low-density polyethylene (LDPE), polyamide (PA), polymethyl methacrylate (PMMA), and glass-slide controls were incubated for five weeks in the coastal waters of four different biogeographic locations (Cape Verde, Chile, Japan, South Africa) during July and August of 2019. The primary driver of the coastal Plastisphere composition was identified as incubation location, i.e., biogeography, while substrate type did not have a significant effect on bacterial community composition. The bacterial communities were consistently dominated by the classes Alphaproteobacteria, Gammaproteobacteria, and Bacteroidia, irrespective of sampling location or substrate type, however a core bacterial Plastisphere community was not observable at lower taxonomic levels. Overall, this study sheds light on the question of whether bacterial communities on plastic debris are shaped by the physicochemical properties of the substrate they grow on or by the marine environment in which the plastics are immersed. This study enhances the current understanding of biogeographic variability in the Plastisphere by including biofilms from plastics incubated in the previously uncharted Southern Hemisphere.

Marine sponges maintain stable bacterial communities between reef sites with different coral to algae cover ratios.

ABSTRACTMarine sponges play a major ecological role in recycling resources on coral reef ecosystems. The cycling of resources may largely depend on the stability of the host–microbiome interactions and their susceptibility to altered environmental conditions. Given the current coral to algal phase shift on coral reefs, we investigated whether the sponge-associated bacterial communities of four sponge species, with either high or low microbial abundances (HMA and LMA), remain stable at two reefs sites with different coral to algae cover ratios. Additionally, we assessed the bacterial community composition of two of these sponge species before and after a reciprocal transplantation experiment between the sites. An overall stable bacterial community composition was maintained across the two sites in all sponge species, with a high degree of host-specificity. Furthermore, the core bacterial communities of the sponges remained stable also after a 21-day transplantation period, although a minor shift was observed in less abundant taxa (< 1%). Our findings support the conclusion that host identity and HMA–LMA status are stronger traits in shaping bacterial community composition than habitat. Nevertheless, long-term microbial monitoring of sponges along with benthic biomass and water quality assessments are needed for identifying ecosystem tolerance ranges and tipping points in ongoing coral reef phase shifts.

Core bacterial community driven the conversion of fulvic acid components during composting with adding manganese dioxide

Here, we revealed the effects of microbes on fulvic acid (FA) formation in composting by adding MnO2. The results showed that the MnO2 promoted the formation of highly humified components (79.2% increased for component 2, and 45.8% increased for component 3) in FA. Additionally, core bacteria involved in FA transformation were identified, the MnO2 increased the relative abundance of core bacteria. Notably, two different core bacteria types were identified: “transforming bacteria” and “processing bacteria”. The “transforming bacteria” dominated (about 40% contribution) in the formation of FA components with a high humification degree. The structural equation model confirmed that “transforming bacteria” could convert partly FA components with low humification into highly humified components, and the “transforming bacteria” could be regulated by environmental factors. These findings provided a new insight to manage FA humification degree during composting and helped to improve the application value of FA.

Microbial Community Succession and Metabolite Changes During Fermentation of BS Sufu, the Fermented Black Soybean Curd by Rhizopus microsporus, Rhizopus oryzae, and Actinomucor elegans

BS Sufu is a fermented food that is made by mixed black soybeans and soybeans. Microbial communities and metabolites play an important role for the final product. We characterized microbial diversity of BS Sufu during fermentation by high-throughput DNA sequencing. Meanwhile, volatile compounds were investigated by solid-phase microextraction (SPME) coupled with gas chromatography–mass spectrometry (GC-MS). The results showed that bacterial diversity was higher than that of fungi in BS Sufu. We found the existence of bacterial and fungal core communities, including Enterococcus, Enterobacter, Rhizopus, and Monascus. Network analysis indicated that bacterial and fungal communities maintain positive and negative interactions, which are important to shape the resident microbial communities in Sufu. In addition, 17 free amino acids (FAAs) were detected at the post-fermentation stage, and umami amino acid mainly contributed to taste of BS Sufu. Furtherly, a total of 79 volatile constituents in BS Sufu, including nine alcohols, 31 esters, and four aldehydes, form synergistically the unique odor of Sufu. Additionally, the correlations between microbiota and metabolites were analyzed. Our results suggested that these microbial taxa and metabolites contribute to the taste and flavor of BS Sufu. This study provided information for analysis of BS Sufu at different fermentation periods in terms of the microbial diversity and metabolites, and this information was important to understand the properties of mixed soybeans Sufu.

Explication of structural variations in the bacterial and archaeal community of anaerobic digestion sludges: An insight through metagenomics

Anaerobic digestion (AD) is a biological process, encompasses the treatment and stabilization of complex organic matter to extract renewable biomethane fuel through microbial interaction in the digester. The main aim of the current study is to investigate the microbial community of anaerobic digestion sludge (ADS), collected at different periods from a mesophilic operating anaerobic digester. The core group of bacteria in ADS including Firmicutes, Bacteroidetes, and Proteobacteria represented more than 60% of the core bacterial community. In ADS (I), the supremacy of Cloacimonetes (18%) was also observed. In ADS (II), the dominance of Anaerobacter (8%) showed the effect of substrate composition on the microbial structure. However, 91% relative abundance of Firmicutes was observed in ADS (III). The hydrogenotrophic methanogens belonging to order Methanomicrobiales and Methanobacteriales exhibited dominance in all three ADSs (> 60%). No specific variations in the archaeal community might be attributed to the presence of beneficial bacterial species. This study provides all the detailed functional roles of microbes involved in AD which can further be used for additional environmental applications.

Seasonal fluctuations in symbiotic bacteria and their role in environmental adaptation of the scleractinian coral Acropora pruinosa in high-latitude coral reef area of the South China Sea

Coral-associated bacterial communities are paramount for coral ecosystems and holobiont health. However, the role of symbiotic bacteria in the adaptation of high-latitude corals to seasonal fluctuations remains underexplored. Therefore, we used 16S rRNA-based high-throughput sequencing to analyze the symbiotic bacterial diversity, composition, and core bacterial community in high-latitude coral and explored the seasonal fluctuation characteristics of symbiotic bacterial communities. We found that bacterial richness and α-diversity changed significantly across different seasons. Additionally, the community structure recombined seasonally, with different dominant bacterial phyla and genera in different seasons. However, the symbiotic bacterial community structures of Acropora pruinosa in winter and spring were similar. Proteobacteria were the dominant bacteria in spring, autumn, and winter. In summer, the dominant bacterial taxa were Bacteroidota and Proteobacteria. Ralstonia was the dominant bacterial genus in spring and winter, whereas in autumn, BD1-7_clade was dominant. Linear discriminant analysis effect size identified 20 abundant genera between the different groups. Core microbiome analysis revealed that 12 core bacterial operational taxonomic units were associated with A. pruinosa in all seasons, seven of which varied with the seasons, changing between dominant and rare. Distance-based redundancy and variation partitioning analyses revealed that sea surface temperature was the major contributor of variation in the microbial community structure. We hypothesized that the high diversity and abundance of symbiotic bacteria and the increase in Prosthecochloris abundance in coral in summer can help A. pruinosa maintain its physiological functions, ameliorating the negative physiological effects of the decrease in Symbiodiniaceae density under high-temperature stress. Thus, the rapid reorganization of the symbiotic bacterial community structure and core microflora in different seasons may allow the corals to adapt to large seasonal environmental fluctuations. In conclusion, seasonal variation of bacteria plays an important role in coral adaptation to large environmental fluctuations.

Distinct microhabitats affect the relative balance of ecological processes shaping the spatial distribution of bacterial communities in lakeshore habitats

Abstract The lakeshore habitat, which is an interface zone between lake and land, harbours various organic particles providing nutrient‐rich microhabitats for bacterial colonisation. Revealing the mechanisms maintaining the bacterial diversity generated on these particles is vital for understanding the biogeochemical processes within lakeshore habitats. To date, however, the bacterial communities within lakeshore habitats have been rarely explored, and knowledge of the ecological processes associated with their spatial distribution is limited. Here, we employed amplicon‐based high throughput sequencing technology to investigate the composition, co‐occurrence patterns, spatial distribution, and assembly processes of free‐living and particle‐attached bacterial communities (FLBC vs. PABC) across 29 lakeshore zones within freshwater lakes from two typical regions: Middle–Lower Yangtze River Plain and Yunnan–Kweichow Plateau. We found significant community dissimilarity between both bacterial lifestyles and regions. PABC exhibited higher community dissimilarity between the plain and plateau regions than FLBC did. Furthermore, eight operational taxonomic units were detected as a core bacterial community within the lakeshore habitats across the plain and plateau regions. Network analysis revealed that bacterial taxa preferring a particle‐attached lifestyle exhibited more co‐occurrence associations for both intra‐ and inter‐community than the free‐living lifestyle. Both FLBC and PABC showed significant distance–decay relationships in these two regions. Dispersal limitation was the most important process associated with patterns in the spatial distribution of FLBC and PABC, whereas the relative importance of variable and homogeneous selection differed between the assembly of FLBC and PABC because of differences in their microhabitats. Our results highlight that dispersal limitation may be strongly associated with the spatial distribution of lakeshore bacterial communities at a regional scale. However, lifestyle differences influence the relative balance between the processes of dispersal, selection, and biotic interaction that influence these bacterial communities. This study reveals potential interactions between bacterial taxa with different lifestyles as well as indicating which ecological processes may lie behind the spatial distribution of bacterial communities in lakeshore habitats. Knowledge of potential assembly mechanisms of bacterial communities within different microhabitats help us understand how bacterial communities in different microhabitats are generated and their different roles in biogeochemical processes in lakeshore habitats.

Exploring benthic cyanobacterial diversity and co-occurring potentially harmful dinoflagellates in six islands of the South Pacific

Cyanobacteria represent a potential risk to human health, as they can produce an array of toxic compounds. Proliferations of potentially toxic benthic marine cyanobacteria are predicted to increase in frequency and spread geographically with climate change and eutrophication, especially in tropical lagoons. Benthic cyanobacterial mats harbour many species of other bacteria and eukaryotic organisms, some of which have been linked to human poisonings after consumption of contaminated seafood. Metabarcoding was used to characterize the taxonomic diversity of 66 benthic cyanobacteria-dominated mats collected from six islands in three different countries of the South Pacific: French Polynesia, the Cook Islands and Kingdom of Tonga. Twenty-five potentially toxic cyanobacteria genera were recorded. Although core bacterial communities (excluding cyanobacteria) remained constant amongst mats, there were significant differences both within and between islands, even when the mats were dominated by the same cyanobacteria genera. Dinoflagellata and Ciliophora were the most dominant eukaryotes and seven potentially toxic genera of dinoflagellates co-occurred in the mats. This is the first baseline survey to use metabarcoding to demonstrate the co-occurrence of potentially toxic marine cyanobacteria and dinoflagellates in the Pacific. The results highlight that further research is needed to evaluate the toxicity of the mats in these regions.

Is core bacterial community more vulnerable to environmental changes in dammed river?

It is well known that dam construction has a potential to impact water quality, resulting other related changes on bacterial community structure and diversity. Yet, effects of dam construction on planktonic and sediment bacterial structure are much more fragmentary. Through sampling of water and sediments along a dammed river between winter and summer, bacterial community were investigated using Illumina high-throughput sequencing. Core bacterial community, including Proteobacteria (55.29%), Firmicutes (25.29%), Bacteroidetes (17.22%), Verrucomicrobia (1.27%) and Gemmatimonadetes (0.93%), were maintained among water and sediments and between seasons. Mantel test showed the core bacterial community was less sensitive to environmental variable. However, a few of dominant microbe, such as class Alphaproteobacteria and family Sphingomonadaceae in core community were still tightly correlated with physiochemical properties according to correlation analysis. Physiochemical characteristics in water and sediment were mainly affected by season fluctuations. Changes in sediment texture has been attributed to the dam construction. This study suggests a potential to detect possible biological indicators of human and natural pressures in riverine system.

Local Geomorphological Gradients and Land Use Patterns Play Key Role on the Soil Bacterial Community Diversity and Dynamics in the Highly Endemic Indigenous Afrotemperate Coastal Scarp Forest Biome.

Southern Afrotemperate forests are small multi-layered and highly fragmented biodiversity rich biomes that support unique flora and fauna endemism. However, little is known about the microbial community and their contribution to these ecosystems. In this study, high throughput sequencing analysis was used to investigate the soil bacterial community structure and function, and understand the effect of local topography/geomorphological formations and land use patterns on a coastal scarp forest. Soil samples were collected from three forest topography sites: upper (steeper gradients, 30–55°; open canopy cover, <30%), mid (less steep, 15–30°; continuous forest canopy, >80%), and lower (flatter gradient, <15°; open canopy cover, 20–65%), and from the adjacent sugarcane farms. Results indicated that forest soils were dominated by members of phyla Proteobacteria (mainly members of α-proteobacteria), Actinobacteria, Acidobacteria, Firmicutes, and Planctomycetes, while Actinobacteria and to a lesser extent β-proteobacteria and γ-proteobacteria dominated SC soils. The core bacterial community clustered by habitat (forest vs. sugarcane farm) and differed significantly between the forest topography sites. The Rhizobiales (genera Variibacter, Bradyrhizobium, and unclassified Rhizobiales) and Rhodospirallales (unclassified Rhodospirillum DA111) were more abundant in forest mid and lower topographies. Steeper forest topography (forest_upper) characterized by the highly leached sandy/stony acidic soils, low in organic nutrients (C and N) and plant densities correlated to significant reduction of bacterial diversity and richness, associating significantly with members of order Burkholderiales (Burkholderia-Paraburkholderia, Delftia, and Massilia) as the key indicator taxa. In contrast, changes in the total nitrogen (TN), soil organic matter (SOM), and high acidity (low pH) significantly influenced bacterial community structure in sugarcane farm soils, with genus Acidothermus (Frankiales) and uncultured Solirubrobacterales YNFP111 were the most abundant indicator taxa. Availability of soil nutrients (TN and SOM) was the strongest driver of metabolic functions related to C fixation and metabolism, N and S cycling; these processes being significantly abundant in forest than sugarcane farm soils. Overall, these results revealed that the local topographical/geomorphological gradients and sugarcane farming affect both soil characteristics and forest vegetation (canopy coverage), that indirectly drives the structure and composition of bacterial communities in scarp forest soils.

Inoculation with rumen fluid in early life accelerates the rumen microbial development and favours the weaning process in goats

BackgroundNewborn ruminants possess an underdeveloped rumen which is colonized by microorganisms acquired from adult animals and the surrounding environment. This microbial transfer can be limited in dairy systems in which newborns are separated from their dams at birth. This study explores whether the direct inoculation of fresh or autoclaved rumen fluid from adult goats to newborn kids has a beneficial effect on rumen microbial development and function.ResultsRepetitive inoculation of young kids with fresh rumen fluid from adult goats adapted to forage (RFF) or concentrate diets (RFC) accelerated microbial colonization of the rumen during the pre-weaning period leading to high protozoal numbers, a greater diversity of bacterial (+ 234 OTUs), methanogens (+ 6 OTUs) and protozoal communities (+ 25 OTUs) than observed in control kids (CTL) without inoculation. This inoculation also increased the size of the core bacterial and methanogens community and the abundance of key rumen bacteria (Ruminococcaceae, Fibrobacteres, Veillonellaceae, Rikenellaceae, Tenericutes), methanogens (Methanobrevibacter ruminantium, Methanomicrobium mobile and Group 9), anaerobic fungi (Piromyces and Orpinomyces) and protozoal taxa (Enoploplastron, Diplodinium, Polyplastron, Ophryoscolex, Isotricha and Dasytricha) before weaning whereas CTL kids remained protozoa-free through the study. Most of these taxa were positively correlated with indicators of the rumen microbiological and physiological development (higher forage and concentrate intakes and animal growth during the post-weaning period) favoring the weaning process in RFF and RFC kids in comparison to CTL kids. Some of these microbiological differences tended to decrease during the post-weaning period, although RFF and RFC kids retained a more complex and matured rumen microbial ecosystem than CTL kids. Inoculation with autoclaved rumen fluid promoted lower development of the bacterial and protozoal communities during the pre-weaning period than using fresh inocula, but it favored a more rapid microbial development during the post-weaning than observed for CTL kids.ConclusionsThis study demonstrated that inoculation of young ruminants with fresh rumen fluid from adult animals accelerated the rumen microbial colonization which was associated with an earlier rumen functional development. This strategy facilitated a smoother transition from milk to solid feed favoring the animal performance during post-weaning and minimizing stress.