Fungicide Effects on Fungal Community Composition in the Wheat Phyllosphere

The fungicides used to control diseases in cereal production can have adverse effects on non-target fungi, with possible consequences for plant health and productivity. This study examined fungicide effects on fungal communities on winter wheat leaves in two areas of Sweden. High-throughput 454 sequencing of the fungal ITS2 region yielded 235 operational taxonomic units (OTUs) at the species level from the 18 fields studied. It was found that commonly used fungicides had moderate but significant effect on fungal community composition in the wheat phyllosphere. The relative abundance of several saprotrophs was altered by fungicide use, while the effect on common wheat pathogens was mixed. The fungal community on wheat leaves consisted mainly of basidiomycete yeasts, saprotrophic ascomycetes and plant pathogens. A core set of six fungal OTUs representing saprotrophic species was identified. These were present across all fields, although overall the difference in OTU richness was large between the two areas studied.     

The needle mycobiome of Picea glauca – A dynamic system reflecting surrounding environment and tree phenological traits

Fungi play a crucial role in terrestrial Arctic ecosystems as symbionts of vascular plants and nutrient recyclers in soil, with many species persistently or temporarily inhabiting the phyllosphere of the vegetation.In this study we apply high-throughput sequencing to investigate the mycobiome of 172 samples of fresh (current year) and aged (3 year old) needles of Picea glauca from three sites over a distance of 500 km in Alaska (USA). We analysed Illumina-generated ITS2 sequences to relate mycobiome data with phenotypic tree traits, measures of genetic variation and climate variables obtained from long-term monitoring of the sites.Alpha-diversity declined with increasing environmental stress/climate harshness. Fungal communities differed in richness and taxonomic composition between sites, with a pronounced difference in the relative abundance of OTUs assigned to species of the rust genus Chrysomyxa, plant pathogens which seem to have been in an outbreak at two sites at the time of sampling.Beside climate parameters, needle age was the second strongest explanatory variable of the mycobiome composition, whereas we found no effect of tree genetic variation, indicating that environmental and tree trait specific variables mainly determined individual white spruce mycobiomes at Alaska's treelines.     

Sources of Resistance to Common Bunt (Tilletia foetida and T. caries) in Durum Wheat

Screening of durum wheat germplasm for resistance to common bunt (Tilletia foetida and T. caries) resulted in the identification of 26 resistant genotypes. The screening was made using nine common bunt isolates from the West Asia and North Africa (WANA) region. In one isolate the two pathogens were represented in ratio of 1:1, whereas eight isolates contained only T. foetida. The correlation, principal components and clustering analyses grouped the genotypes into three clusters., Cluster one comparised genotypes close to Senatore (S.) Cappelli and Haurani, the latter is a landrace from Syria. Cluster three comprised advanced genotypes containing resistance genes from Mindum, a Turkish landrace. Results indicated that donor sources of resistance appear to be related to the three major sources mentioned. Cultivar S. Cappelli is considered resistant since it has been grown by farmers on a large scale for many years and remained resistant to common bunt throughout 7 years of testing. This resistance is assumed to be of a durable type. The isolates were also grouped into three clusters representing different ecological areas and the wheat types from which the isolates originated. We infer that the different clusters reflect the presence of three pathotype groups of the pathogens.     

Culturable mycobiome of soya bean cyst nematode (Heterodera glycines) cysts from a long-term soya bean-corn rotation system is dominated by Fusarium

The cyst of the soya bean cyst nematode (SCN; Heterodera glycines), an economically important pathogen of soya beans worldwide, represents a unique microhabitat in soil. The fungi inhabiting cysts may include natural antagonists of the SCN as well as saprotrophs and other opportunists. This study aimed to characterise the entire culturable mycobiome of SCN cysts obtained from a long-term soya bean-corn rotation experiment using ITS fungal barcoding. Fusarium was consistently the most frequently isolated taxon across all sampling time points and crop sequences, followed by Ilyonectria. Among fourteen genera frequently isolated from SCN cysts, five fell within the single family Nectriaceae (Sordariomycetes) and five within the order Pleosporales (Dothideomycetes), suggesting independent evolutionary origins and shared adaptations in these groups towards colonisation of SCN cysts. Six genera (Pochonia, Clonostachys, Fusarium, Neonectria, Alternaria, and Leptosphaeria) varied significantly by crop sequence in at least one year.     

节肢动物α-淀粉酶系统进化树构建及分析

目的:构建节肢动物α-淀粉酶的系统进化树,探讨其进化关系,找出进化树中聚类在一起的α-淀粉酶的特异性序列。方法:在美国国立生物技术信息中心(National Center for Biotechnology Information,NCBI)数据库中选取了56个节肢动物的α-淀粉酶氨基酸序列,利用CLUSTALX2.0进行序列比对、MEGA6.0建立进化树,通过BOXSHADE找到聚类的α-淀粉酶特异性序列。结果:56个α-淀粉酶聚类成A、B、C、D四大簇,A簇特异性序列为"VD NHD NQ",B簇特异性序列为"ID NHD NX",C簇特异性序列为"ID NHD NQ",D簇特异性序列为"XGN NHD X"。A、B、C、D四簇都含有保守的NHD(天冬酰胺-组氨酸-天冬氨酸)序列,但序列两端氨基酸种类不同。结论:56个节肢动物α-淀粉酶分为4簇,每簇都有其特异性序列,但都含有保守序列NHD。     

Rheological and breadmaking properties of wheat samples infected with<Emphasis Type="Italic">Fusarium spp.</Emphasis>

Rheological and breadmaking properties of untreated and suboptimally stored wheat samples (grain moisture: 20%, temperature: 20°C) and also of wheat which was inoculated withFusarium spp. were investigated. The deoxynivalenol (DON) content of the stored and inoculated wheat samples ranged between 820–12,000 μg/kg. Gluten proteins were isolated with different extraction solutions and the fractions obtained were analysed by means of RP-HPLC. Microextension tests and micro-baking tests were used for the determination of dough properties (maximum resistance (MR) and extensibility (EX)) and bread volume, respectively. In spite of the extremely high DON concentrations of some wheat samples contaminated withFusarium spp. they showed only a slight decrease of the amount of gluten proteins. Extension tests of dough led to a slight decrease of MR, bread volumes stayed almost the same compared with the non-contaminated grain. The contamination of wheat withAspergillus andPenicillium led to a high decrease of gluten proteins, which resulted in an extremely decreased MR of the dough and a very low bread volume.     

Distribution and Diversity of Archaea Corresponding to the Limnological Cycle of a Hypersaline Stratified Lake (Solar Lake, Sinai, Egypt)

The vertical and seasonal distribution and diversity of archaeal sequences was investigated in a hypersaline, stratified, monomictic lake, Solar Lake, Sinai, Egypt, during the limnological development of stratification and mixing. Archaeal sequences were studied via phylogenetic analysis of 16S rDNA sequences as well as denaturing gradient gel electrophoresis analysis. The 165 clones studied were grouped into four phylogenetically different clusters. Most of the clones isolated from both the aerobic epilimnion and the sulfide-rich hypolimnion were defined as cluster I, belonging to the Halobacteriaceae family. The three additional clusters were all isolated from the anaerobic hypolimnion. Cluster II is phylogenetically located between the genera Methanobacterium and Methanococcus. Clusters III and IV relate to two previously documented groups of uncultured euryarchaeota, remotely related to the genus Thermoplasma. No crenarchaeota were found in the water column of the Solar Lake. The archaeal community in the Solar Lake under both stratified and mixed conditions was dominated by halobacteria in salinities higher than 10%. During stratification, additional clusters, some of which may possibly relate to uncultured halophilic methanogens, were found in the sulfide- and methane-rich hypolimnion.     

Genomic analysis and secondary metabolite production in Bacillus amyloliquefaciens AS 43.3: A biocontrol antagonist of Fusarium head blight

The complete genome of the biocontrol antagonist Bacillus amyloliquefaciens AS 43.3 is reported. B. amyloliquefaciens AS 43.3 has previously been shown to be effective in reducing Fusarium head blight in wheat. The 3.9 Mbp genome was sequenced, assembled, and annotated. Genomic analysis of the strain identified 9 biosynthetic gene clusters encoding secondary metabolites associated with biocontrol activity. The analysis identified five non-ribosomal peptide synthetase clusters encoding three lipopeptides (surfactin, iturin, and fengycin), a siderophore (bacillibactin), and the antibiotic dipeptide bacilysin. In addition, three polyketide synthetase clusters were identified which encoded for the antibacterials: bacillaene, difficidin, and macrolactin. In addition to the non-ribosomal mediated biosynthetic clusters discovered, we identified a ribosomally encoded biosynthetic cluster that produces the antibiotic plantazolicin. To confirm the gene clusters were functional, cell-free culture supernatant was analyzed using LC–MS/MS. The technique confirmed the presence of all nine metabolites or their derivatives. The study suggests the strain is most likely a member of the B. amyloliquefaciens subsp. plantarium clade. Comparative genomics of eight completed genomes of B. amyloliquefaciens identify the core and pan-genomes for the species, including identifying genes unique to the biocontrol strains. This study demonstrates the growing importance of applying genomic-based studies to biocontrol organisms of plant pathogens which can enable the rapid identification of bioactive metabolites produced by a prospective biological control organism. In addition, this work provides a foundation for a mechanistic understanding of the B. amyloliquefaciens AS 43.3/Fusarium head blight biocontrol interaction.     

Fungal community composition in the gut of rove beetles (Coleoptera: Staphylinidae) from the Canadian boreal forest reveals possible endosymbiotic interactions for dietary needs

The goal of this study was to investigate the fungal community composition in the gut of Staphylinidae from boreal forest in order to better understand the diversity and the complexity of fungus-insect relationships. DNA gut content analyses of nine abundant rove beetle species (Coleoptera, Staphylinidae) living in the boreal balsam fir forest ecosystem (Montmorency Forest, Quebec, Canada) were performed to identify the fungal taxa present either as endosymbiotic taxa or as a source of nutrition. A total of 42 fungal operational taxonomic units (OTUs) were recorded from the analysis of 441 fungal ITS rDNA sequences recovered from gut extracts. The OTU richness per species ranged between four in Tachinus quebecensis and 16 in Atheta ventricosa. The fungal mycobiota in posterior gut extracts was dominated by Saccharomycetales (12 OTUs), followed by Sordariomycetes (nine OTUs). No significant difference was observed between the OTU richness recorded within each of the three subfamilies of rove beetles investigated. The core mycobiome of the posterior gut extracts was dominated by three OTUs related to yeasts, with ITS sequences having pairwise similarities equal to or greater than 99% with Candida mesenterica, Debaryomyces spp. and Ophiostoma pluriannulatum. These results provide some evidence of the consumer-resource relationships of these beetles. Predominance of yeast and fungal spores in the posterior gut of rove beetles suggests that they may play an important role in their dietary requirements and as endosymbionts.     

Fungal tolerance to Congo red,a cell wall integrity stress,as a promising indicator of ecological niche

Differential sensitivities to the cell wall stress caused by Congo red (CR) have been observed in many fungal species. In this study, the tolerances and sensitivities to CR was studied with an assorted collection of fungal species from three phylogenetic classes: Sordariomycetes, Dothideomycetes, and Eurotiomycetes, three orders, and eight families. These grouped into different ecological niches, such as insect pathogens, plant pathogens, saprotrophs, and mycoparasitics. The saprotroph Aspergillus niger and the mycoparasite Trichoderma atroviride stood out as the most resistant species to cell wall stress caused by CR, followed by the plant pathogenic fungi, a mycoparasite, and other saprotrophs. The insect pathogens had low tolerance to CR. The insect pathogens Metarhizium acridum and Cordyceps fumosorosea were the most sensitive to CR. In conclusion, Congo red tolerance may reflect ecological niche, accordingly, the tolerances of the fungal species to Congo red were closely aligned with their ecology.     

Impacts of poultry house environment on poultry litter bacterial community composition

Viral and bacterial pathogens are a significant economic concern to the US broiler industry and the ecological epicenter for poultry pathogens is the mixture of bedding material, chicken excrement and feathers that comprises the litter of a poultry house. This study used high-throughput sequencing to assess the richness and diversity of poultry litter bacterial communities, and to look for connections between these communities and the environmental characteristics of a poultry house including its history of gangrenous dermatitis (GD). Cluster analysis of 16S rRNA gene sequences revealed differences in the distribution of bacterial phylotypes between Wet and Dry litter samples and between houses. Wet litter contained greater diversity with 90% of total bacterial abundance occurring within the top 214 OTU clusters. In contrast, only 50 clusters accounted for 90% of Dry litter bacterial abundance. The sixth largest OTU cluster across all samples classified as an Arcobacter sp., an emerging human pathogen, occurring in only the Wet litter samples of a house with a modern evaporative cooling system. Ironically, the primary pathogenic clostridial and staphylococcal species associated with GD were not found in any house; however, there were thirteen 16S rRNA gene phylotypes of mostly gram-positive phyla that were unique to GD-affected houses and primarily occurred in Wet litter samples. Overall, the poultry house environment appeared to substantially impact the composition of litter bacterial communities and may play a key role in the emergence of food-borne pathogens.     

AFLPs are incompatible with RAPD and morphological data in Pennisetum purpureum (Napier grass)

Accessions of Pennisetum purpureum in agricultural research centres in sub-Saharan Africa were genotyped using Amplified Fragment Length Polymorphisms (AFLPs) using primer combinations MluI/MseI. Cluster analyses of resulting bands suggested that the samples could be grouped into five large and five small-sized clusters. Principal coordinate analysis revealed two major clusters being well separated, with bulk of the samples forming one, poorly structured cluster. Our analyses failed to reveal the regional groupings found in previous studies using a subset of our sample universe and based on RAPDs as well as morphological and agronomical data. The inability of the AFLP data to clearly demarcate accessions is ascribed to either the presence of high levels of genetic uniformity, or non-optimal primers and/or bad germplasm management practices. The re-registration of all accessions, based on DNA barcoding, is suggested as a means to resolve the lingering problems regarding the identity of accessions.     

Identification of a Core Bacterial Community within the Large Intestine of the Horse

The horse has a rich and complex microbial community within its gastrointestinal tract that plays a central role in both health and disease. The horse receives much of its dietary energy through microbial hydrolysis and fermentation of fiber predominantly in the large intestine/hindgut. The presence of a possible core bacterial community in the equine large intestine was investigated in this study. Samples were taken from the terminal ileum and 7 regions of the large intestine from ten animals, DNA extracted and the V1-V2 regions of 16SrDNA 454-pyrosequenced. A specific group of OTUs clustered in all ileal samples and a distinct and different signature existed for the proximal regions of the large intestine and the distal regions. A core group of bacterial families were identified in all gut regions with clear differences shown between the ileum and the various large intestine regions. The core in the ileum accounted for 32% of all sequences and comprised of only seven OTUs of varying abundance; the core in the large intestine was much smaller (5-15% of all sequences) with a much larger number of OTUs present but in low abundance. The most abundant member of the core community in the ileum was Lactobacillaceae, in the proximal large intestine the Lachnospiraceae and in the distal large intestine the Prevotellaceae. In conclusion, the presence of a core bacterial community in the large intestine of the horse that is made up of many low abundance OTUs may explain in part the susceptibility of horses to digestive upset.     

454 Pyrosequencing reveals bacterial diversity of activated sludge from 14 sewage treatment plants

Activated sludge (AS) contains highly complex microbial communities. In this study, PCR-based 454 pyrosequencing was applied to investigate the bacterial communities of AS samples from 14 sewage treatment plants of Asia (mainland China, Hong Kong, and Singapore), and North America (Canada and the United States). A total of 259 K effective sequences of 16S rRNA gene V4 region were obtained from these AS samples. These sequences revealed huge amount of operational taxonomic units (OTUs) in AS, that is, 1183–3567 OTUs in a sludge sample, at 3% cutoff level and sequencing depth of 16 489 sequences. Clear geographical differences among the AS samples from Asia and North America were revealed by (1) cluster analyses based on abundances of OTUs or the genus/family/order assigned by Ribosomal Database Project (RDP) and (2) the principal coordinate analyses based on OTUs abundances, RDP taxa abundances and UniFrac of OTUs and their distances. In addition to certain unique bacterial populations in each AS sample, some genera were dominant, and core populations shared by multiple samples, including two commonly reported genera of Zoogloea and Dechloromonas, three genera not frequently reported (i.e., Prosthecobacter, Caldilinea and Tricoccus) and three genera not well described so far (i.e., Gp4 and Gp6 in Acidobacteria and Subdivision3 genera incertae sedis of Verrucomicrobia). Pyrosequencing analyses of multiple AS samples in this study also revealed the minority populations that are hard to be explored by traditional molecular methods and showed that a large proportion of sequences could not be assigned to taxonomic affiliations even at the phylum/class levels.     

Fungal palaeodiversity revealed using high‐throughput metabarcoding of ancient DNA from arctic permafrost

The taxonomic and ecological diversity of ancient fungal communities was assessed by combining next generation sequencing and metabarcoding of DNA preserved in permafrost. Twenty‐six sediment samples dated 16 000–32 000 radiocarbon years old from two localities in Siberia were analysed for fungal ITS. We detected 75 fungal OTUs from 21 orders representing three phyla, although rarefaction analyses suggested that the full diversity was not recovered despite generating an average of 6677 ± 3811 (mean ± SD) sequences per sample and that preservation bias likely has considerable effect on the recovered DNA. Most OTUs (75.4%) represented ascomycetes. Due to insufficient sequencing depth, DNA degradation and putative preservation biases in our samples, the recovered taxa probably do not represent the complete historic fungal community, and it is difficult to determine whether the fungal communities varied geographically or experienced a composition shift within the period of 16 000–32 000 bp . However, annotation of OTUs to functional ecological groups provided a wealth of information on the historic communities. About one‐third of the OTUs are presumed plant‐associates (pathogens, saprotrophs and endophytes) typical of graminoid‐ and forb‐rich habitats. We also detected putative insect pathogens, coprophiles and keratinophiles likely associated with ancient insect and herbivore faunas. The detection of putative insect pathogens, mycoparasites, aquatic fungi and endophytes broadens our previous knowledge of the diversity of fungi present in Beringian palaeoecosystems. A large group of putatively psychrophilic/psychrotolerant fungi was also detected, most likely representing a modern, metabolically active fungal community.     

The fungal community associated with the ambrosia beetle Xylosandrus compactus invading the mediterranean maquis in central Italy reveals high biodiversity and suggests environmental acquisitions

In summer 2016 a severe infestation of the alien ambrosia beetle Xylosandrus compactus was recorded from the Mediterranean maquis in the Circeo National Park in Central Italy. Trees and shrubs were infested and displayed wilting and necrosis of terminal branches caused by the combined impact of the insect and associated pathogenic fungi. A preliminary screening carried out on captured adults resulted in the isolation of a discrete number of fungal taxa with different life strategies, ranging from true mutualist (e.g. Ambrosiella xylebori) to plant pathogens (Fusarium spp.). In the present study, high-throughput sequencing was applied to determine the total diversity and functionality of the fungal community associated with X. compactus adults collected in the galleries of three Mediterranean woody hosts, Quercus ilex, Laurus nobilis, and Ceratonia siliqua. The effect of season and host in determining the composition of the associated fungal community was investigated. A total of 206 OTUs composed the fungal community associated with X. compactus. Eighteen OTUs were shared among the three hosts, including A. xylebori and members of the Fusarium solani complex. All but two were previously associated with beetles.Sixty-nine out of 206 OTUs were resolved to species level, identifying 60 different fungal species, 22 of which already reported in the literature as associated with beetles or other insects. Functional guild assigned most of the fungal species to saprotrophs and plant pathogens. Effects of seasonality and host on fungal community assemblage were highlighted suggesting the acquisition by the insect of new fungal taxa during the invasion process. The consequences of enriched fungal community on the risk of the insurgence of novel threatful insect–fungus association are discussed considering direct and indirect effects on the invaded habitat.     

Differences Between Barley, Oats and Wheat in the Occurrence of Deoxynivalenol and Other Trichothecenes in Norwegian Grain

The amount of the Fusarium toxins deoxynivalenol (DON). 3-acety-DON. ivalenol and fusarenon × have been determined in about 3000 samples of barley, oats and wheat grown in Norway. The samples were collected in the period 1988–1994. and grouped according to grain species, year of production, district and sample category. The DON content was found to be significantly higher in oats than both barley and wheat in grain produced by ordinary grain producers in Norway. Of samples collected from grain silos. 68.7% of the barley. 97.1% of the oats and 66.3% of the wheat samples were found to contain 30 mg/kg of DON or more. The proportion containing 1000 μg kg or more was 2.1.13.4and0.0% in burley, oats and wheat, respectively. However, these variations in contamination level were not reflected in the results from two field trials, where the grain species were grown side-by-side in the same fields. The differences in contamination level between the grain species seem to be due partly to edaphic and agrotechnical factors and partly to variation in the susceptibility to different Fusarium species in interaction with climatic factors. Nivalenol(≥ 50 μg/kg) was detected in 8.3% of the barley samples. 8.2% of the oats and 0.4% of the wheat samples. Samples collected at the grain silos were then not included.     

Fish gut microbiota analysis differentiates physiology and behavior of invasive Asian carp and indigenous American fish

Gut microbiota of invasive Asian silver carp (SVCP) and indigenous planktivorous gizzard shad (GZSD) in Mississippi river basin were compared using 16S rRNA gene pyrosequencing. Analysis of more than 440 000 quality-filtered sequences obtained from the foregut and hindgut of GZSD and SVCP revealed high microbial diversity in these samples. GZSD hindgut (GZSD_H) samples (n=23) with >7000 operational taxonomy units (OTUs) exhibited the highest alpha-diversity indices followed by SVCP foregut (n=15), GZSD foregut (n=9) and SVCP hindgut (SVCP_H) (n=24). UniFrac distance-based non-metric multidimensional scaling (NMDS) analysis showed that the microbiota of GZSD_H and SVCP_H were clearly separated into two clusters: samples in the GZSD cluster were observed to vary by sampling location and samples in the SVCP cluster by sampling date. NMDS further revealed distinct microbial community between foregut to hindgut for individual GZSD and SVCP. Cyanobacteria, Proteobacteria, Actinobacteria and Bacteroidetes were detected as the predominant phyla regardless of fish or gut type. The high abundance of Cyanobacteria observed was possibly supported by their role as the fish''s major food source. Furthermore, unique and shared OTUs and OTUs in each gut type were identified, three OTUs from the order Bacteroidales, the genus Bacillariophyta and the genus Clostridium were found significantly more abundant in GZSD_H (14.9–22.8%) than in SVCP_H (0.13–4.1%) samples. These differences were presumably caused by the differences in the type of food sources including bacteria ingested, the gut morphology and digestion, and the physiological behavior between GZSD and SVCP.     

Fungal community associated with adults of the chestnut gall wasp Dryocosmus kuriphilus after emergence from galls: Taxonomy and functional ecology

The diversity of the fungal community associated with adults of Dryocosmus kuriphilus following emergence was examined using HTS analysis. Ascomycota dominated the fungal core-biome community. The functional guilds of the 90 taxa forming the core-biome were assessed, demonstrating three main groups: saprotrophs, plant pathogens and entomopathogens. Twenty-nine OTUs out of 90 were resolved to species level identifying 26 different fungal species. Among these species, many were cosmopolitan or previously recorded in Europe. Ten taxa were previously recorded on chestnut, including some recognized plant pathogens associated with foliage and green tissues such as Epicoccum nigrum, Gnomoniopsis castanea, Colletotrichum acutatum, Stromatoseptoria castaneicola, Ramularia endophylla. Beauveria bassiana; within the core microbiome, Fusarium larvarum represented the most abundant entomopathogenic species. Some of these species are known to impact directly or indirectly the vitality of the insects in the galls. The chestnut blight pathogen, Cryphonectria parasitica, was never found associated with D. kuriphilus. Based on the present study, an active role for D. kuriphilus as a vector of chestnut fungal endophyte/pathogens cannot be demonstrated but neither ruled out.     

Diversity of Bacterial Biofilm Communities on Sprinklers from Dairy Farm Cooling Systems in Israel

On dairy farms in hot climates worldwide, cows suffer from heat stress, which is alleviated by the use of water cooling systems. Sprinklers and showerheads are known to support the development of microbial biofilms, which can be a source of infection by pathogenic microorganisms. The aim of this study was to investigate the presence of microbial biofilms in dairy cooling systems, and to analyze their population compositions using culture-independent technique, 16S rRNA gene sequencing. Biofilm samples were collected on eight dairy farms from 40 sprinklers and the microbial constituents were identified by deep sequencing of the 16S rRNA gene. A total of 9,374 operational taxonomic units (OTUs) was obtained from all samples. The mean richness of the samples was 465 ± 268 OTUs which were classified into 26 different phyla; 76% of the reads belonged to only three phyla: Proteobacteria, Actinobacteria and Firmicutes. Although the most prevalent OTUs (Paracoccus, Methyloversatilis, Brevundimonas, Porphyrobacter, Gp4, Mycobacterium, Hyphomicrobium, Corynebacterium and Clostridium) were shared by all farms, each farm formed a unique microbial pattern. Some known potential human and livestock pathogens were found to be closely related to the OTUs found in this study. This work demonstrates the presence of biofilm in dairy cooling systems which may potentially serve as a live source for microbial pathogens.