Quantifying the relative roles of selective and neutral processes in defining eukaryotic microbial communities

We have a limited understanding of the relative contributions of different processes that regulate microbial communities, which are crucial components of both natural and agricultural ecosystems. The contributions of selective and neutral processes in defining community composition are often confounded in field studies because as one moves through space, environments also change. Managed ecosystems provide an excellent opportunity to control for this and evaluate the relative strength of these processes by minimising differences between comparable niches separated at different geographic scales. We use next-generation sequencing to characterize the variance in fungal communities inhabiting adjacent fruit, soil and bark in comparable vineyards across 1000 kms in New Zealand. By compartmentalizing community variation, we reveal that niche explains at least four times more community variance than geographic location. We go beyond merely demonstrating that different communities are found in both different niches and locations by quantifying the forces that define these patterns. Overall, selection unsurprisingly predominantly shapes these microbial communities, but we show the balance of neutral processes also have a significant role in defining community assemblage in eukaryotic microbes

Variable Copy Number, Intra-Genomic Heterogeneities and Lateral Transfers of the 16S rRNA Gene in Pseudomonas

Even though the 16S rRNA gene is the most commonly used taxonomic marker in microbial ecology, its poor resolution is still not fully understood at the intra-genus level. In this work, the number of rRNA gene operons, intra-genomic heterogeneities and lateral transfers were investigated at a fine-scale resolution, throughout the Pseudomonas genus. In addition to nineteen sequenced Pseudomonas strains, we determined the 16S rRNA copy number in four other Pseudomonas strains by Southern hybridization and Pulsed-Field Gel Electrophoresis, and studied the intra-genomic heterogeneities by Denaturing Gradient Gel Electrophoresis and sequencing. Although the variable copy number (from four to seven) seems to be correlated with the evolutionary distance, some close strains in the P. fluorescens lineage showed a different number of 16S rRNA genes, whereas all the strains in the P. aeruginosa lineage displayed the same number of genes (four copies). Further study of the intra-genomic heterogeneities revealed that most of the Pseudomonas strains (15 out of 19 strains) had at least two different 16S rRNA alleles. A great difference (5 or 19 nucleotides, essentially grouped near the V1 hypervariable region) was observed only in two sequenced strains. In one of our strains studied (MFY30 strain), we found a difference of 12 nucleotides (grouped in the V3 hypervariable region) between copies of the 16S rRNA gene. Finally, occurrence of partial lateral transfers of the 16S rRNA gene was further investigated in 1803 full-length sequences of Pseudomonas available in the databases. Remarkably, we found that the two most variable regions (the V1 and V3 hypervariable regions) had probably been laterally transferred from another evolutionary distant Pseudomonas strain for at least 48.3 and 41.6% of the 16S rRNA sequences, respectively. In conclusion, we strongly recommend removing these regions of the 16S rRNA gene during the intra-genus diversity studies

Structure of the parasite infracommunity of Sciades proops from the Japaratuba River Estuary, Sergipe, Brazil

Abstract The catfish species Sciades proops inhabits muddy estuaries and shallow brackish lagoons, as well as freshwater. For these reasons, it is believed that this species may act as an intermediate, definitive and paratenic host in the life cycle of many parasites. From November 2010 to November 2011 and from August 2012 to July 2013, a total of 126 specimens of Sciades proops from the estuarine region of the Japaratuba River in the state of Sergipe, Brazil, were examined for parasites, of which 84.13% were infected by at least one species: Ergasilus sp. (Copepoda) (Prevalence P = 77.78%, Mean of Intensity MI = 10.08 ± 15.48, Mean Abundance MA = 14.27 ± 7.48) in the gills, Contracaecum sp. (P = 23.02%, MI = 20.59 ± 80.58, MA =39.12 ± 4.47) in the general cavity, Procamallanus sp. (P = 0.79%, MI = 1, MA = 0.01 ± 0.09), Raphidascaroides sp. (P = 2.31%, MI = 1.33 ± 0.58, MA = 0.33 ± 0.22) and Cuccullanus sp. (Nematoda) (P = 0.79%, MI = 1, MA = 0.01 ± 0.09) in the intestine, Ancyrocephalinae (Monogenea) (P = 0.79%, MI = 1, MA = 0.01 ± 0.09) in the gills, Pseudoacanthostomumpanamense (P = 1.59%, MI = 9.00 ± 8.49, MA = 0.14 ± 1.36) in the intestine, Clinostomum sp. (P = 1.59%, MI = 17.50 ± 23.33, MA = 0.29 ± 3.03) on the body surface and two unidentified metacercariae, referred to as Metacercaria 1 (P = 0.79%; IM = 1, MA = 0.01 ± 0.09) and Metacercaria 2 (Digenea) (P = 0.79%, MI = 7, MA = 0.06 ± 0.62) in the swim bladder. Ergasilus sp. was the dominant species and thus classified as core, with Contracaecum sp. as the satellite and other species as secondary species. The spatial distribution of infection with Ergasilus sp. and Contracaecum sp. showed a typical pattern of aggregate distribution. The sex of the host did not influence parasitic infections, but infection with Ergasilus sp. showed a positive and significant correlation with biometric and epidemiologic parameters, whereas infection with Contracaecum sp. was correlated only with prevalence and abundance

Structure of the parasite infracommunity of Sciades proops from the Japaratuba River Estuary, Sergipe, Brazil

Abstract The catfish species Sciades proops inhabits muddy estuaries and shallow brackish lagoons, as well as freshwater. For these reasons, it is believed that this species may act as an intermediate, definitive and paratenic host in the life cycle of many parasites. From November 2010 to November 2011 and from August 2012 to July 2013, a total of 126 specimens of Sciades proops from the estuarine region of the Japaratuba River in the state of Sergipe, Brazil, were examined for parasites, of which 84.13% were infected by at least one species: Ergasilus sp. (Copepoda) (Prevalence P = 77.78%, Mean of Intensity MI = 10.08 ± 15.48, Mean Abundance MA = 14.27 ± 7.48) in the gills, Contracaecum sp. (P = 23.02%, MI = 20.59 ± 80.58, MA =39.12 ± 4.47) in the general cavity, Procamallanus sp. (P = 0.79%, MI = 1, MA = 0.01 ± 0.09), Raphidascaroides sp. (P = 2.31%, MI = 1.33 ± 0.58, MA = 0.33 ± 0.22) and Cuccullanus sp. (Nematoda) (P = 0.79%, MI = 1, MA = 0.01 ± 0.09) in the intestine, Ancyrocephalinae (Monogenea) (P = 0.79%, MI = 1, MA = 0.01 ± 0.09) in the gills, Pseudoacanthostomumpanamense (P = 1.59%, MI = 9.00 ± 8.49, MA = 0.14 ± 1.36) in the intestine, Clinostomum sp. (P = 1.59%, MI = 17.50 ± 23.33, MA = 0.29 ± 3.03) on the body surface and two unidentified metacercariae, referred to as Metacercaria 1 (P = 0.79%; IM = 1, MA = 0.01 ± 0.09) and Metacercaria 2 (Digenea) (P = 0.79%, MI = 7, MA = 0.06 ± 0.62) in the swim bladder. Ergasilus sp. was the dominant species and thus classified as core, with Contracaecum sp. as the satellite and other species as secondary species. The spatial distribution of infection with Ergasilus sp. and Contracaecum sp. showed a typical pattern of aggregate distribution. The sex of the host did not influence parasitic infections, but infection with Ergasilus sp. showed a positive and significant correlation with biometric and epidemiologic parameters, whereas infection with Contracaecum sp. was correlated only with prevalence and abundance

Anisakidae Skrjabin & Karokhin, 1945 and Raphidascarididae Hartwich, 1954 nematodes in lutjanidae (pisces: perciformes) from the Brazilian Northeast Coast

Abstract The present study aimed at describing and evaluating the fauna of Anisakidae and Raphidacarididae nematodes of lutjanid fish (snappers) from the Brazilian northeastern coast unloaded at the city of Aracaju, capital of the State of Sergipe. A total of 186 lutjanids of 5 different species were analyzed including 69 Lutjanus analis, 51 L. vivanus , 29 Ocyurus chrysurus, 23 L. synagris, and 14 L. jocu. Nematode specimens found in the viscera of these fish were clarified with lactophenol. Illustrations of each of these specimens were prepared to help identify these samples and compose their taxonomic description and classification. At necropsy, 3,183 nematodes belonging to two families were collected from fish viscera which included the following: Anisakidae: Anisakis, Terranova , Contracaecum, and Goezia; Raphidascarididae: Raphidascaris (Ichthyascaris) and Hysterothylacium . A total of six genera of nematodes were found at postmortem examination of which adult worms of only three genera (Goezia, Raphidascaris and Hysterothylacium) were detected in the fish examined. Larvae of Terranova sp. were found only in the musculature of O. chrysurus . Most of the nematode larvae were present in the mesentery and organs of the fish necropsied. Therefore, the zoonotic potential of these nematodes cannot be ruled out. There was a significant negative correlation between the intensity of parasitism by anisakids and the total body length of O. chrysurus; the intensity of parasitism was greater in smaller and shortef fish. There was a significant positive correlation between the abundance of these parasites and the length of L. synagris; the presence of these parasites increased according to the fish’s body length. To the authors’ knowledge, these are the first records of Raphidascaris (Ichthyascaris ) sp. and Hysterothylacium sp. in L. vivanus , of Terranova sp. in O. chrysurus and L. jocu, and of Goezia sp. in L. analis. These novel findings add the Brazilian northeast coast and the State of Sergipe in the geographic distribution of these parasites in the country

Kudoa spp. (Myxozoa, Multivalvulida) parasitizing fish caught in Aracaju, Sergipe, Brazil.

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The microbiome beyond the horizon of ecological and evolutionary theory

The ecological and evolutionary study of community formation, diversity, and stability is rooted in general theory and reinforced by decades of system-specific empirical work. Deploying these ideas to study the assembly, complexity, and dynamics of microbial communities living in and on eukaryotes has proved seductive, but challenging. The success of this research endeavour depends on our capacity to observe and characterize the distributions, abundances, and functional traits of microbiota, representing an array of technical and analytical challenges. Furthermore, a number of unique characteristics of microbial species, such as horizontal gene transfer, the production of public goods, toxin and antibiotic production, rapid evolution, and feedbacks between the microbiome and its host, are not easily accommodated by current ecological and evolutionary theory. Here we highlight potential pitfalls in the application of existing theoretical tools without careful consideration of the unique complexities of the microbiome, focusing particularly on the issue of human health, and anchoring our discussion in existing empirical evidence