Core Microbial Community Research Articles

Dispersal Limitation Expands the Diversity of Coral Microbiome Metacommunity in the South China Sea

The coral microbiome is one of the most complex microbial biospheres. However, the ecological processes shaping coral microbiome community assembly are not well understood. Here, we investigated the abundance, diversity, and community assembly mechanisms of coral-associated microbes from a highly diverse coral metacommunity in the South China Sea. Compared to seawater, the coral microbial metacommunity were defined by highly variable bacterial abundances among individual coral samples, high species evenness but not high species richness, high β-diversity, and a small core microbiome. We used variation partitioning analysis, neutral community model, and null model to disentangle the influences of different ecological processes in coral microbiome assembly. Measured physico-chemical parameters of the surrounding seawater and the spatial factor together explained very little of the variation in coral microbiome composition. Neutral processes only explained a minor component of the variation of coral microbial communities, suggesting a non-stochastic community assembly. Homogeneous and heterogeneous selection, but not dispersal, contributed greatly to the assembly of the coral microbiome. Such selection could be attributed to the within-host environments rather than the local environments. Our results demonstrated that dispersal limitation and host filtering contribute significantly to the assembly of discrete coral microbial regimes and expand the metacommunity diversity.

Specific dissolved organic matter components drive the assembly of a core microbial community in acidic soil of ammonium-preferring plants

Interactions among plant species, soil type and microorganisms in terrestrial ecosystem are extremely complex and still rather limited. Here, we examined the relationship in plant–microbe-soil system by the effect of soil dissolved organic matter on the associated rhizosphere microbial community and potential function. Soil samples of Hapludults were collected from acidic subtropical forest soil in Longhu Mountain in Jiangxi Province of China. Treatments with plants (three ammonium-preferring plants: sugarcane, tea, and lespedeza) and without plants (control) were operated in acidic subtropical soil for 28 days. Gas chromatography-mass spectrometry (GC–MS) and high-throughput sequencing were applied to investigate the dissolved organic matter (DOM) and microbial community structure. The results showed that the largest contributions of 23 specific DOM (mainly organic acids, sugars, and amino acids) involved in different pathways of nitrogen metabolism, arginine metabolism, and cyanoamino acid metabolism, were significantly up-regulated 2–30 times in planted soils compared with the control (p < 0.05). Additionally, the predominant microorganisms of bacteria Acidobacteria (30.4%), Solibacteres (5.67%), Deltaproteobacteria (3.12%), and Betaproteobacteria (9.95%) in class level, as well as fungi Clitopilus (1.34%) and Mortierella (54.58%) in genera level, were enriched in planted soils. Furthermore, the enriched groups positively correlated between the 23 DOM and nitrogen transformation function (gross rate of NO3− assimilation, heterotrophic nitrification and plant uptake of nitrogen, p < 0.05), suggesting that ammonium-preferring plants recruit soil microbiota by releasing organic substrates and the core microbiota aid plant nutrient uptake and protect plants from potential pathogens in acidic subtropical soil.

Monitoring Infection and Antibiotic Treatment in the Skin Microbiota of Farmed European Seabass (Dicentrarchus Labrax) Fingerlings.

The microbiota of fish skin, the primary barrier against disease, is highly dynamic and modulated by several factors. In fish aquaculture, disease outbreaks occur mainly during early-life stages, with associated high economic losses. Antibiotic treatments sometimes remain the best option to control bacterial diseases, despite many reported negative impacts of its use on fish and associated microbiota. Notwithstanding, studies monitoring the effects of disease and antibiotic treatment on the microbiota of fingerlings are scarce. We sequenced the bacterial 16S rRNA V4 gene region using a metabarcoding approach to assess the impact of a mixed infection with Photobacterium damselae ssp. piscicida and Vibrio harveyi and subsequent antibiotic treatment with flumequine, on the skin microbiota of farmed seabass (Dicentrarchus labrax) fingerlings. Both infection and antibiotic treatment led to a significant increase in bacterial diversity and core microbial communities and impacted microbiome structure. Dysbiosis was confirmed by changes in the abundance of potential pathogenic and opportunistic bacterial taxa. Skin bacterial metabolic function was also significantly affected by flumequine administration, suggesting a detriment to fish skin health. Our results add to an increasing body of literature, showing how fish microbiome response to infection and antibiotics cannot be easily predicted.

Biochar addition reduces nitrogen loss and accelerates composting process by affecting the core microbial community during distilled grain waste composting

This study evaluated the impact of biochar addition on nitrogen (N) loss and the process period during distilled grain waste (DGW) composting. Results from the five treatments (0, 5, 10, 15, and 20% biochar addition) indicated that 10% biochar addition (DB10) was optimal, resulting in the lowest N loss, 25.69% vs. 40.01% in the control treatment. Moreover, the DGW composting period was shortened by approximately 14 days by biochar addition. The composition of the microbial community was not significantly altered with biochar addition in each phase, however, it did accelerate the microbial succession during DGW composting. N metabolism pathway prediction revealed that biochar addition enhanced nitrification and inhibited denitrification, and the latter phenomenon was the main reason for reducing N loss during DGW composting. Based on the above results, a potential mechanism model for biochar addition to reduce N loss during the DGW composting process was established.

Evaluation of humic acid conversion during composting under amoxicillin stress: Emphasizes the driving role of core microbial communities

This study aimed to investigate the effects of various amoxicillin (AMX) concentrations on humic acid (HA) formation and the bacterial community structure (BCS) during chicken manure aerobic composting. The findings showed that AMX caused a rise in pH and a shortening of the thermophilic cycle during the thermophilic period. Moreover, a high concentration of AMX (150 mg/kg) inhibited community succession and humification at maturity. In addition to influencing environmental factors, AMX increased the relative abundance (RA) of the dominant bacteria in the thermophilic phase (Firmicutes) and decreased the RA of the dominant bacteria in the mature phase (Proteobacteria). From carbon conversion, AMX promoted fulvic acid (FA) anabolism in the early period and inhibited HA accumulation in the later period. As a result, the primary impact of AMX on HA transformation was the alteration of the BCS, ultimately affecting the quality of compost.

Micro-morphological Characteristics of Particles on Holly and Ligustrum Leaf Surfaces and Seasonal Changes in Bacterial Communities

The characteristics of particles and microorganisms on leaf surfaces have great significance for the near-surface environment and ecology. Here, fresh leaves of holly and Ligustrum were examined from different functional areas in Qingdao. Environmental scanning electron microscopy was used to observe particles and microorganisms on the leaf surfaces during different seasonal, and Illumina high-throughput sequencing was performed to analyze the phyllosphere bacterial community structure. The results showed that the retention of TSP on leaves in autumn and winter was higher than in spring and summer. The leaves of the two plants were more likely to retain PM10 and PM2.5; however, the dust retention capacity of holly leaves was higher than that of Ligustrum, especially for particle sizes greater than 10 μm. The numbers of particles on the leaf surfaces along an urban main road were higher than in two other locations, and were greatly affected by ground dust and automobile exhaust emissions. The community structure of phyllospheric microorganisms showed distinct seasonal variation, with different types of fungi, fungal spores, and mycelium observed on the leaf surfaces. Mycelium was more frequently detected on leathery leaves, and fungal spores with even folds were detected on the leaf epidermis of Ligustrum. The relative abundances of phyllospheric microorganisms were highest on leaves from an urban park, explained by a positive effect of humidity on growth. Significant differences in bacterial community abundance were observed between seasons. Specifically, bacterial abundance was highest in spring and lowest in summer. γ-Proteobacteria were the dominant bacteria, and the two plants shared a similar core microbial community. In addition, the phyllospheric bacterial community structure of leaves from urban arterial roads with ground dust pollution was significantly different from the leaves collected from other city areas. Our research results suggest a significant correlation between the leaf-surface particles and microbial community structure on representative plants in different areas of the city, which provides reference information for urban greening activities.

Marine signature taxa and core microbial community stability along latitudinal and vertical gradients in sediments of the deepest freshwater lake.

Lake Baikal is the deepest (~1.6 km) and most voluminous freshwater reservoir on Earth. Compared to plankton, its benthos remains poorly explored. Here, we ask whether latitude and/or depth determine benthic microbial community structure and how Baikal communities compare to those of other freshwater, brackish and marine sediments. To answer, we collected sediment upper layers (0-1 cm) across a ~600 km North-South transect covering the three basins of the lake and from littoral to bathybenthic depths (0.5-1450 m). Analysis of 16S and 18S rRNA gene amplicon sequences revealed communities with high richness and evenness where rare operational taxonomic units (OTUs) collectively dominated. Archaea represented up to 25% or prokaryotic sequences. Baikal sediments harbored typically marine eukaryotic and prokaryotic OTUs recently identified in some lakes (diplonemids, Bolidophyceae, Mamiellales, SAR202, marine-like Synechococcus, Pelagibacterales) but also SAR324, Syndiniales and Radiolaria. We hypothesize that, beyond the salinity barrier, adaptation to oligotrophy explains the presence of these otherwise typically marine lineages. Baikal core benthic communities were relatively stable across sites and seemed not determined by depth or latitude. Comparative analyses with other freshwater, brackish and marine prokaryotic sediment communities confirmed the distinctness of Baikal benthos, which include elements of similarity to marine and hydrothermally influenced systems.

Seed-borne, endospheric and rhizospheric core microbiota as predictors of plant functional traits across rice cultivars are dominated by deterministic processes.

A host-plant and its associated microbiota depend on one another. However, the assembly process and the functioning of host-associated microbiota are poorly understood. Herein, rice was used as model plant to investigate the assemblage of bacterial microbiota, including those in the seed, root endosphere and rhizosphere. We also assessed the degree to which endosphere and rhizosphere communities were influenced by vertical transmission through seed and identified the core microbes that potentially associated with plant phenotypic properties. Plant microhabitat, rather than subspecies type, was the major driver shaping plant-associated bacterial microbiota. Deterministic processes were primarily responsible for community assembly in all microhabitats. The influence of vertical transmission from seed to root-associated bacterial communities appeared to be quite weak (endosphere) or even absent (rhizosphere). A core microbial community composed of 15 generalist species persisted across different microhabitats and represented key connectors in networks. Host-plant functional traits were linked to the relative abundance of these generalist core microbes and could be predicted from them using machine learning algorithms. Overall, bacterial microbiota is assembled by host-plant interactions in a deterministic-based manner. This study enhances our understanding of the driving mechanisms and associations of microbiota in various plant microhabitats and provides new perspectives to improve plant performance.

Microbial community structure shifts and potential Symbiodinium partner bacterial groups of bleaching coral Pocillopora verrucosa in South China Sea.

The community structure of coral associated microorganisms will change greatly in coral bleaching. However, the relationship between specific bacteria groups and Symbiodinium, which is easy to be found in the bleaching process, has been ignored for a long time. In this study, the changes of coral microbial community during a natural bleaching event in the South China Sea were studied by 16S rRNA gene high-throughput sequencing. The microbial community composition of bleached corals was significantly different from that of normal corals (P < 0.001). OTUs belong to Bacillus, Exiguobacterium, Oceanobacillus, Saccharibacteria and Ostreobiaceae was significantly increased in the bleaching corals. The relative abundance of 30.9% OTUS changed significantly during coral bleaching. The relative abundance of potential coral pathogenic groups was not significantly different between normal and bleaching corals. Symbiodinium positively correlated bacterial groups accounted for 6.9% and 4.3% in the normal corals and bleached corals, respectively. The dominated groups of potential Symbiodinium-partner bacteria are Lactococcus and Bacillus. The potential Symbiodinium-partner bacterial groups in bleached corals were significantly lower than that in the normal corals, which further showed their coexistence with Symbiodinium. This study provides insight into the role of potential Symbiodinium-partner bacterial groups in the coral bleaching process and supports the theory of beneficial microorganisms for corals.

CPR and DPANN Have an Overlooked Role in Corals' Microbial Community Structure.

Understanding how microbial communities are structured in coral holobionts is important to estimate local and global impacts and provide efficient environment management strategies. Several studies investigated the relationship between corals and their microbial communities, including the environmental drivers of shifts in this relationship, associated with diseases and coral cover loss. However, these studies are often geographically or taxonomically restricted and usually focused on the most abundant microbial groups, neglecting the rare biosphere, including archaea in the group DPANN and the recently discovered bacterial members of the candidate phyla radiation (CPR). Although it is known that rare microbes can play essential roles in several environments, we still lack understanding about which taxa comprise the rare biosphere of corals' microbiome. Here, we investigated the host-related and technical factors influencing coral microbial community structure and the importance of CPR and DPANN in this context by analyzing more than a hundred coral metagenomes from independent studies worldwide. We show that coral genera are the main biotic factor shaping coral microbial communities. We also detected several CPR and DPANN phyla comprising corals' rare biosphere for the first time and showed that they significantly contribute to shaping coral microbial communities.

Microbiome diversity and evolution in stacking fermentation during different rounds of Jiang-flavoured Baijiu brewing

Microbiome during stacking fermentation is one of the most important factors in Jiang-flavoured (Moutai - flavour) Baijiu brewing, as it determines the yield and quality. Here, high-throughput sequencing and statistical analysis were performed to analyse the diversity and succession of microbial communities during stacking fermentation for seven rounds. In total, 27 bacterial phyla and 658 genera and seven fungal phyla and 156 genera were identified in 26 composite samples obtained from 130 individual samples. Although the microbial communities were rich and varied in the seven rounds, several genera were highly stable, including core bacterial genera, i.e., Bacillus (13.32%–31.98%), Lentibacillus (1.08%–28.79%), Kroppenstedtia (0.68%–24.02%), Oceanobacillus (0.11%–11.04%), and Lactobacillus (0.43%–26.41%) and core fungal genera, i.e., Thermomyces (9.48%–53.21%), Byssochlamys (1.8%–52.14%), Thermoascus (5.75%–28.26%), unclassified_o_Eurotiales (4.04%–24.35%), and Aspergillus (0.15%–9.58%). Each round also had its own characteristic microbial genera. Fermentation parameters (starch, moisture, acidity, and reducing sugar) were related to core and characteristic microbial community succession. The core microbial communities affect the fermentation parameters, and fermentation parameters regulate the characteristic microbiome. This study may help improve the understanding of the evolution of microbial community and the relationships between microbiota and fermentation parameters in stacking fermentation during Jiang-flavoured Baijiu brewing.

Evaluation of nitrogen conversion pathway during composting under amoxicillin stress: Mainly driven by core microbial community

The aim of this study was to explore the effects of different concentrations of amoxicillin (AMX) on nitrogen (N) conversion and bacterial community structure during aerobic composting. The results revealed that AMX led to a lower temperature and increased pH during the thermophilic phase of composting. AMX inhibited the relative abundance (RA) of Firmicutes at the initial phase but increased the RA of Actinobacteria and Bacteroidetes compared with the control treatment. The core bacterial community linked to N conversion was determined by network analysis. AMX decreased the RA of amoA, a gene related to nitrification, and increased the RAs of nirK and nosZ, which are related to denitrification. Meanwhile, AMX inhibited the activity of ammonia-oxidizing bacteria but promoted the activity of denitrifying bacteria. Therefore, the main adverse effect of AMX on compost quality is to change the microbial community structure and affect the physical and chemical properties of composting.

The bacterial and fungal communities associated with Anthurium ssp. leaves: Insights into plant endemism and microbe association

It is known that different plant species select specific microbes to live inside their tissues in a process determined by the host genotype, phenotype and geographic location, which can introduce discussion on plant endemism and the assembly of specific microbial communities. Herein, we report the results of an investigation relating the geographic distribution of plant species and the composition of microbial communities associated with plant hosts. The bacterial and fungal community associated with Anthurium plant leaves was mapped to assess the diversity and ecology of the endophytic community associated with Anthurium spp. collected on islands and on the Brazilian mainland. Twenty-six Anthurium specimens were surveyed, distributed throughout the São Paulo state coastline, including Alcatrazes Island, some coastal islands and distinct mainland environments. Bacterial and fungal endophytes were obtained from the leaves of A. alcatrazense, A. loefgrenii, A. penthaphyllum, A. urvellianum and A. intermedium and subjected to massive bacterial 16S rRNA and fungal ITS sequencing. The results indicated that A. alcatrazense, endemic to Alcatrazes Island, hosted a specific bacterial community structure, while its fungal community was similar to that of Anthurium species from other locations. Betaproteobacteria showed a high differential occurrence in A. alcatrazense. Some groups of fungi were found mainly inhabiting A. loefgrenii plants. While Alphaproteobacteria, Gammaproteobacteria, Actinobacteria and Sordariomycetes, Dothiodeomycetes and Tremellomycetes composed the core microbial community among Anthurium plants. The results suggest crucial role for the bacterial communities to endemic plants, while endophytic fungal diversity is less specifically distributed among endemic and nonendemic plant species.

Core microbial communities of lacustrine microbialites sampled along an alkalinity gradient.

Microbialites are usually carbonate-rich sedimentary rocks formed by the interplay of phylogenetically and metabolically complex microbial communities with their physicochemical environment. Yet, the biotic and abiotic determinants of microbialite formation remain poorly constrained. Here, we analysed the structure of prokaryotic and eukaryotic communities associated with microbialites occurring in several crater lakes of the Trans-Mexican volcanic belt along an alkalinity gradient. Microbialite size and community structure correlated with lake physicochemical parameters, notably alkalinity. Although microbial community composition varied across lake microbialites, major taxa-associated functions appeared quite stable with both, oxygenic and anoxygenic photosynthesis and, to less extent, sulphate reduction, as major putative carbonatogenic processes. Despite interlake microbialite community differences, we identified a microbial core of 247 operational taxonomic units conserved across lake microbialites, suggesting a prominent ecological role in microbialite formation. This core mostly encompassed Cyanobacteria and their typical associated taxa (Bacteroidetes, Planctomycetes) and diverse anoxygenic photosynthetic bacteria, notably Chloroflexi, Alphaproteobacteria (Rhodobacteriales, Rhodospirilalles), Gammaproteobacteria (Chromatiaceae) and minor proportions of Chlorobi. The conserved core represented up to 40% (relative abundance) of the total community in lakes Alchichica and Atexcac, displaying the highest alkalinities and the most conspicuous microbialites. Core microbialite communities associated with carbonatogenesis might be relevant for inorganic carbon sequestration purposes.

Evolving the core microbial community in pit mud based on bioturbation of fortified Daqu.

Directional stress is an effective measure to change the community structure and improve the bioactivity of pit mud (PM). In this study, the addition of fortified Daqu to artificial PM (APM) was intended to disturb the microbial community and further affect metabolites. To evaluate the effect of fortified Daqu on culturing APM, the microbial communities of APM with or without the addition of fortified Daqu were investigated by fluorescence in situ hybridization and Illumina MiSeq. The results indicated that microbes (Clostridium sp., Clostridium kluyveri, hydrogenotrophic methanogens, and acetotrophic methanogens) related to the production of key aroma compounds increased notably when fortified Daqu was added. In particular, the hydrogenotrophic and acetotrophic methanogens increased by 6.19- and 4.63-fold after 30days of culture. Subsequently, metabolites (organic acids, volatile compounds) were also analyzed by HPLC (high-performance liquid chromatography) and HS-SPME-GC-MS (headspace solid phase microextraction - gas chromatography - mass spectrometry). The results showed that the content of butyric acid and hexanoic acid was significantly higher when fortified Daqu was added to APM. In addition, the proportion of esters and phenols was also higher than in APM without fortified Daqu. A survey of the microbial compositions of APMs with or without added fortified Daqu indicated that the microbial community evolves into a functional community favoring liquor brewing. We have developed a novel process by disturbing the community diversity.

Anti-quorum sensing activity of some marine bacteria isolated from different marine resources in Egypt.

To screen for a variety of marine bacteria with anti-quorum sensing and anti-biofilm activities. Among 188 bacterial isolates from water, sediment, and corals in the Red Sea region, approximately 35% (65 isolates) of the isolates displayed a significant degradation in the purple pigment of the bioreporter strain without affecting cell growth. The quorum quenching bacteria obtained from coral-associated bacteria were 66.2% out of the total isolates. The PCR amplification results revealed that the recorded Acyl Homoserine lactone (AHL) inhibition by 91% of the anti-QS marine bacteria was not due to lactonase activity. On the other hand, lactonase genes were recorded only in the remaining 9% (6 isolates) and those were belonging to genus Bacillus, Nocardiopsis, and Enterobacter based on 16S rRNA gene sequences. The results also showed that marine bacteria with anti-QS activity inhibited 67% of the biofilm formed by Aeromonas hydrophila, Pseudomonas aeruginosa, and Vibrio alginolyticus. The computational profiling analysis confirmed the presence of the functional region in the detected genes. Coral microbial communities are rich sources for pharmacologically important natural products with anti-quorum sensing and anti-biofilm activities.

Reducing host DNA contamination in 16S rRNA gene surveys of anthozoan microbiomes using PNA clamps

Efforts to study the microbial communities associated with corals can be limited by inefficiencies in the sequencing process due to high levels of host amplification by universal bacterial 16S rRNA gene primers. Here, we develop an inexpensive peptide nucleic acid (PNA) clamp that binds to a target sequence of host DNA during PCR and blocks amplification. We then test the ability of this PNA clamp to mitigate host contamination and increase overall microbial sequence coverage on samples from three coral species: the gorgonians Eunicea flexuosa and Gorgonia ventalina, and the scleractinian Porites panamensis. The 20-bp PNA clamp was designed using DNA from E. flexuosa. Adding the PNA clamp during PCR increased the percentage of microbial reads in E. flexuosa samples more than 11-fold. Microbial community diversity was similar without- and with-PNA clamps, as were the relative frequencies of the ten most abundant ASVs (amplicon sequence variants), indicating that the clamps successfully blocked host DNA amplification while simultaneously increasing microbial DNA amplification proportionally across the most abundant taxa. The reduction of E. flexuosa DNA correlated with an increase in the abundance of rarer taxa. The clamp also increased the average percentage of microbial reads in another gorgonian, G. ventalina, by 8.6-fold without altering the microbial community beta diversity, and in a distantly related scleractinian coral, P. panamensis, by nearly double. The reduction of host contamination correlated with the number of nucleotide mismatches between the host amplicon and the PNA clamp. The PNA clamp costs as little as $0.48 per sample, making it an efficient and cost-effective solution to increase microbial sequence coverage for high-throughput sequencing of coral microbial communities.

Oxytetracycline stress reconstruct the core microbial community related to nitrogen transformation during composting

This study investigated oxytetracycline (OTC) effects on nitrogen (N) transformation and bacterial community diversity during chicken manure composting. The addition of OTC inhibited nitrifying bacteria, resulted in a decrease in the transformation of NH4+-N to NO3−-N during composting, and affected in the order T3 (32.76%) > T2 (28.76%) > T1 (17.02%) > CK. The OTC could act as an inhibitor against core microbial growth, leading to a delay effect during composting. 16S rRNA sequencing was employed for the functional prediction, and results indicated the bacterial community related to N transformation reconstructed under OTC stress. The core microorganisms were changed after OTC addition, with the emergence of Bacillus and Thermobifida, which could inhibit the N transformation by network analysis. Therefore, core microorganisms could be regulated to reduce the negative of OTC impacts on N transformation and thus reduce N loss during composting.

Nutrient utilization efficiency, ruminal fermentation and microbial community in Holstein bulls fed concentrate-based diets with different forage source

Ruminal acidosis can penalize cattle performance and modify ruminal microbiota composition; in that sense, providing quality forage may be a useful tool to cope with such dysfunction. This assay aimed to control animals’ performance and assess ruminal microbiota shifts and interactions when fattening Holstein bulls are fed corn-based concentrate and different quality forages. Thirty animals (from 119 to 332 d of age and from 164 to 511 kg body weight [BW]) were fed corn-based concentrate and were allotted to three experimental treatments or forage sources: barley straw, considered as control (Hordeum vulgare, CTR), oats haylage (Avena sativa, OATS) or vetch haylage (Vicia sativa, VETCH). Both concentrate and forage were supplied ad libitum in a free choice system and animals had free access to drinking water. Bulls’ BW and concentrate intake were automatically recorded on a daily basis. Feces and ruminal fluid were sampled twice, during the growing period (158 d of age and 220 kg BW) and during the finishing period (280 d of age and 434 kg BW), for digestibility, ruminal fermentation and microbial population characterization. No differences in concentrate intake or BW could be detected between CTR and OATS-fed animals; however, VETCH-fed bulls had lower concentrate intake (P < 0.047) and slaughter BW (P = 0.034) than CTR. The use of oats haylage as forage source did not affect nutrient apparent digestibility rates but vetch haylage did penalize dry matter (P = 0.048) and crude protein (P < 0.001) digestibility in finishing animals. Differences in neither ruminal volatile fatty acids concentration nor pH were detected, but acetate-to-propionate ratio increased with the incorporation of vetch haylage in diet (P < 0.041). Ammonia-nitrogen concentration in ruminal fluid was low (20.63 ± 2.55 mg/L) but it significantly improved when oats (P = 0.001, only in finishing) and vetch (P = 0.001) haylage were provided. Core microbial community gathered 75 % of analyzed sequences; however, ruminal microbial community was different between CTR and OATS (P < 0.001) or VETCH (P < 0.001) bulls. Shannon and Simpson diversity indexes were improved by quality forage feeding, mainly during the growing period (P < 0.081 in OATS and P < 0.004 in VETCH). Microbial network analysis revealed that the use of oats or vetch haylage promoted an increase in the overall network complexity, basically in terms of node degree and betweenness centrality. Some lactate-degrader genera were found to be central nodes in the microbial network when quality forage was provided, highlighting their probable implication in ruminal acidosis prevention.

The microbial ecology of a Mediterranean chlorinated drinking water distribution systems in the city of Valencia (Spain)

Drinking water distribution systems host extensive microbiomes with diverse biofilm communities regardless of treatment, disinfection, or operational practices. In Mediterranean countries higher temperatures can accelerate reactions and microbial growth that may increase aesthetic water quality issues, particularly where material deposits can develop as a result of net zero flows within looped urban networks. This study investigated the use of flow and turbidity monitoring to hydraulically manage mobilisation of pipe wall biofilms and associated material from the Mediterranean city of Valencia (Spain). Pipe sections of different properties were subjected to controlled incremental flushing with monitoring and sample collection for physico-chemical and DNA analysis with Illumina sequencing of bacterial and fungal communities. A core microbial community was detected throughout the network with microorganisms like Pseudomonas, Aspergillus or Alternaria increasing during flushing, indicating greater abundance in underlying and more consolidated material layers. Bacterial and fungal communities were found to be highly correlated, with bacteria more diverse and dynamic during flushing whilst fungi were more dominant and less variable between sampling sites. Results highlight that water quality management can be achieved through hydraulic strategies yet understanding community dynamics, including the fungal component, will be key to maintaining safe and ultimately beneficial microbiomes in drinking water distribution systems.