Microbiome succession during ammonification in eelgrass bed sediments
Background Eelgrass (Zostera marina) is a marine angiosperm and foundation species that plays an important ecological role in primary production, food web support, and elemental cycling in coastal ecosystems. As with other plants, the microbial communities living in, on, and near eelgrass are thought to be intimately connected to the ecology and biology of eelgrass. Here we characterized the microbial communities in eelgrass sediments throughout an experiment to quantify the rate of ammonification, the first step in early remineralization of organic matter, also known as diagenesis, from plots at a field site in Bodega Bay, CA. Methods Sediment was collected from 72 plots from a 15 month long field experiment in which eelgrass genotypic richness and relatedness were manipulated. In the laboratory, we placed sediment samples (n = 4 per plot) under a N2 atmosphere, incubated them at in situ temperatures (15 °C) and sampled them initially and after 4, 7, 13, and 19 days to determine the ammonification rate. Comparative microbiome analysis using high throughput sequencing of 16S rRNA genes was performed on sediment samples taken initially and at seven, 13 and 19 days to characterize changes in the relative abundances of microbial taxa throughout ammonification. Results Within-sample diversity of the sediment microbial communities across all plots decreased after the initial timepoint using both richness based (observed number of OTUs, Chao1) and richness and evenness based diversity metrics (Shannon, Inverse Simpson). Additionally, microbial community composition changed across the different timepoints. Many of the observed changes in relative abundance of taxonomic groups between timepoints appeared driven by sulfur cycling with observed decreases in predicted sulfur reducers (Desulfobacterales) and corresponding increases in predicted sulfide oxidizers (Thiotrichales). None of these changes in composition or richness were associated with variation in ammonification rates. Discussion Our results showed that the microbiome of sediment from different plots followed similar successional patterns, which we infer to be due to changes related to sulfur metabolism. These large changes likely overwhelmed any potential changes in sediment microbiome related to ammonification rate. We found no relationship between eelgrass presence or genetic composition and the microbiome. This was likely due to our sampling of bulk sediments to measure ammonification rates rather than sampling microbes in sediment directly in contact with the plants and suggests that eelgrass influence on the sediment microbiome may be limited in spatial extent. More in-depth functional studies associated with eelgrass microbiome will be required in order to fully understand the implications of these microbial communities in broader host-plant and ecosystem functions (e.g., elemental cycling and eelgrass-microbe interactions).
Ettinger et al. (2017) Microbiome succession during ammonification in eelgrass bed sediments. PeerJ 5:e3674 https://doi.org/10.7717/peerj.3674
RNA helicase domains of viral origin in proteins of insect retrotransposons: possible source for evolutionary advantages
Recently, a novel phenomenon of horizontal gene transfer of helicase-encoding sequence from positive-stranded RNA viruses to LINE transposons in insect genomes was described. TRAS family transposons encoding an ORF2 protein, which comprised all typical functional domains and an additional helicase domain, were found to be preserved in many families during the evolution of the order Lepidoptera. In the present paper, in species of orders Hemiptera and Orthoptera, we found helicase domain-encoding sequences integrated into ORF1 of retrotransposons of the Jockey family. RNA helicases encoded by transposons of TRAS and Jockey families represented separate brunches in a phylogenetic tree of helicase domains and thus could be considered as independently originated in the evolution of insect transposons. Transcriptome database analyses revealed that both TRAS and Jockey transposons encoding the helicase domain represented transcribed genome sequences. Moreover, the transposon-encoded helicases were found to contain the full set of conserved motifs essential for their enzymatic activities. Taking into account the previously reported ability of RNA helicase encoded by TRAS ORF2 to suppress post-transcriptional RNA silencing, we propose possible scenarios of evolutionary fixation of actively expressed functional helicases of viral origin in insect retrotransposons as genetic elements advantageous for both transposons and their insect hosts.
Morozov et al. (2017) RNA helicase domains of viral origin in proteins of insect retrotransposons: possible source for evolutionary advantages. PeerJ 5:e3673 https://doi.org/10.7717/peerj.3673
Changes in zooplankton community, and seston and zooplankton fatty acid profiles at the freshwater/saltwater interface of the Chowan River, North Carolina
The variability in zooplankton fatty acid composition may be an indicator of larval fish habitat quality as fatty acids are linked to fish larval growth and survival. We sampled an anadromous fish nursery, the Chowan River, during spring of 2013 in order to determine how the seston fatty acid composition varied in comparison with the zooplankton community composition and fatty acid composition during the period of anadromous larval fish residency. The seston fatty acid profiles showed no distinct pattern in relation to sampling time or location. The mesozooplankton community composition varied spatially and the fatty acid profiles were typical of freshwater species in April. The Chowan River experienced a saltwater intrusion event during May, which resulted in brackish water species dominating the zooplankton community and the fatty acid profile showed an increase in polyunsaturated fatty acids (PUFA), in particular eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA). The saltwater intrusion event was followed by an influx of freshwater due to high precipitation levels in June. The zooplankton community composition once again became dominated by freshwater species and the fatty acid profiles shifted to reflect this change; however, EPA levels remained high, particularly in the lower river. We found correlations between the seston, microzooplankton and mesozooplankton fatty acid compositions. Salinity was the main factor correlated to the observed pattern in species composition, and fatty acid changes in the mesozooplankton. These data suggest that anadromous fish nursery habitat likely experiences considerable spatial variability in fatty acid profiles of zooplankton prey and that are correlated to seston community composition and hydrodynamic changes. Our results also suggest that sufficient prey density as well as a diverse fatty acid composition is present in the Chowan River to support larval fish production.
Lichti et al. (2017) Changes in zooplankton community, and seston and zooplankton fatty acid profiles at the freshwater/saltwater interface of the Chowan River, North Carolina. PeerJ 5:e3667 https://doi.org/10.7717/peerj.3667
RNA expression and disease tolerance are associated with a “keystone mutation” in the ochre sea star Pisaster ochraceus
An overdominant mutation in an intron of the elongation factor 1-α (EF1A) gene in the sea star Pisaster ochraceus has shown itself to mediate tolerance to “sea star wasting disease”, a pandemic that has significantly reduced sea star populations on the Pacific coast of North America. Here we use RNA sequencing of healthy individuals to identify differences in constitutive expression of gene regions that may help explain this tolerance phenotype. Our results show that individuals carrying this mutation have lower expression at a large contingent of gene regions. Individuals without this mutation also appear to have a greater cellular response to temperature stress, which has been implicated in the outbreak of sea star wasting disease. Given the ecological significance of P. ochraceus, these results may be useful in predicting the evolutionary and demographic future for Pacific intertidal communities.
Chandler et al. (2017) RNA expression and disease tolerance are associated with a “keystone mutation” in the ochre sea star Pisaster ochraceus. PeerJ 5:e3696 https://doi.org/10.7717/peerj.3696
Germination of dimorphic seeds of Suaeda aralocaspica in response to light and salinity conditions during and after cold stratification
Cold stratification is a requirement for seed dormancy breaking in many species, and thus it is one of the important factors for the regulation of timing of germination. However, few studies have examined the influence of various environmental conditions during cold stratification on subsequent germination, and no study has compared such effects on the performance of dormant versus non-dormant seeds. Seeds of halophytes in the cold desert might experience different light and salinity conditions during and after cold stratification. As such, dimorphic seeds (non-dormant brown seeds and black seeds with non-deep physiological dormancy) of Suaeda aralocaspica were cold stratified under different light (12 h light–12 h darkness photoperiod or continuous darkness) or salinity (0, 200 or 1,000 mmol L-1 NaCl) conditions for 20 or 40 days. Then stratified seeds were incubated under different light or salinity conditions at daily (12/12 h) temperature regime of 10:25 °C for 20 days. For brown seeds, cold stratification was also part of the germination period. In contrast, almost no black seeds germinated during cold stratification. The longer the cold stratification, the better the subsequent germination of black seeds, regardless of light or salinity conditions. Light did not influence germination of brown seeds. Germination of cold-stratified black seeds was inhibited by darkness, especially when they were stratified in darkness. With an increase in salinity at the stage of cold stratification or germination, germination percentages of both seed morphs decreased. Combinational pre-treatments of cold stratification and salinity did not increase salt tolerance of dimorphic seeds in germination phase. Thus, light and salinity conditions during cold stratification partly interact with these conditions during germination stage and differentially affect germination of dimorphic seeds of S. aralocaspica.
Wang et al. (2017) Germination of dimorphic seeds of Suaeda aralocaspica in response to light and salinity conditions during and after cold stratification. PeerJ 5:e3671 https://doi.org/10.7717/peerj.3671
Aura-biomes are present in the water layer above coral reef benthic macro-organisms
As coral reef habitats decline worldwide, some reefs are transitioning from coral- to algal-dominated benthos with the exact cause for this shift remaining elusive. Increases in the abundance of microbes in the water column has been correlated with an increase in coral disease and reduction in coral cover. Here we investigated how multiple reef organisms influence microbial communities in the surrounding water column. Our study consisted of a field assessment of microbial communities above replicate patches dominated by a single macro-organism. Metagenomes were constructed from 20 L of water above distinct macro-organisms, including (1) the coral Mussismilia braziliensis, (2) fleshy macroalgae (Stypopodium, Dictota and Canistrocarpus), (3) turf algae, and (4) the zoanthid Palythoa caribaeorum and were compared to the water microbes collected 3 m above the reef. Microbial genera and functional potential were annotated using MG-RAST and showed that the dominant benthic macro-organisms influence the taxa and functions of microbes in the water column surrounding them, developing a specific “aura-biome”. The coral aura-biome reflected the open water column, and was associated with Synechococcus and functions suggesting oligotrophic growth, while the fleshy macroalgae aura-biome was associated with Ruegeria, Pseudomonas, and microbial functions suggesting low oxygen conditions. The turf algae aura-biome was associated with Vibrio, Flavobacterium, and functions suggesting pathogenic activity, while zoanthids were associated with Alteromonas and functions suggesting a stressful environment. Because each benthic organism has a distinct aura-biome, a change in benthic cover will change the microbial community of the water, which may lead to either the stimulation or suppression of the recruitment of benthic organisms.
Walsh et al. (2017) Aura-biomes are present in the water layer above coral reef benthic macro-organisms. PeerJ 5:e3666 https://doi.org/10.7717/peerj.3666
The age of onset of substance use is related to the coping strategies to deal with treatment in men with substance use disorder
Background The age of onset of substance use (OSU) as well as the coping strategies (CS) influence both the development and the course of Substance Use Disorders (SUD). We aim to examine the differences in the CS applied to deal with treatment in men with SUD, considering whether the age of OSU had begun at age 16 or earlier (OSU ≤ 16) or at 17 years or later (OSU ≥ 17), as well as the associations of the CS with clinical variables were studied. Methods A total of 122 patients with at least three months of abstinence, 60 with OSU≤16 and 62 with OSU≥17, were evaluated through the Coping Strategies Inventory and clinical assessment tools. Results The OSU≤16 patients were younger and presented a worse clinical state. Compared to the norms, the SUD patients were less likely to use adaptive CS, although this was more remarkable for the OSU≤16 group. Furthermore, the OSU≤16 patients presented a CS pattern of higher Disengagement, with lesser use of Social Support and higher Problem Avoidance and Social Withdrawal. In the whole SUD sample, the severity of addiction, number of relapses and age of OSU (as a continuous variable) were related to maladaptive coping. Nevertheless, the cut-off age of OSU modulated these results. Conclusions The OSU≤16 was a risk factor for presenting greater clinical severity and a more dysfunctional CS profile to deal with treatment. Thus, the cut-off age considered has allowed us to differentiate SUD patients with more vulnerability to present worse clinical prognosis who may require specific prevention and rehabilitation strategies discussed throughout this work.
Capella et al. (2017) The age of onset of substance use is related to the coping strategies to deal with treatment in men with substance use disorder. PeerJ 5:e3660 https://doi.org/10.7717/peerj.3660
Biological effects of carbon nanotubes generated in forest wildfire ecosystems rich in resinous trees on native plants
Carbon nanotubes (CNTs) have a broad range of applications and are generally considered human-engineered nanomaterials. However, carbon nanostructures have been found in ice cores and oil wells, suggesting that nature may provide appropriate conditions for CNT synthesis. During forest wildfires, materials such as turpentine and conifer tissues containing iron under high temperatures may create chemical conditions favorable for CNT generation, similar to those in synthetic methods. Here, we show evidence of naturally occurring multiwalled carbon nanotubes (MWCNTs) produced from Pinus oocarpa and Pinus pseudostrobus, following a forest wildfire. The MWCNTs showed an average of 10 walls, with internal diameters of ∼2.5 nm and outer diameters of ∼14.5 nm. To verify whether MWCNT generation during forest wildfires has a biological effect on some characteristic plant species of these ecosystems, germination and development of seedlings were conducted. Results show that the utilization of comparable synthetic MWCNTs increased seed germination rates and the development of Lupinus elegans and Eysenhardtia polystachya, two plants species found in the burned forest ecosystem. The finding provides evidence that supports the generation and possible ecological functions of MWCNTs in nature.
Lara-Romero et al. (2017) Biological effects of carbon nanotubes generated in forest wildfire ecosystems rich in resinous trees on native plants. PeerJ 5:e3658 https://doi.org/10.7717/peerj.3658
Beyond the carapace: skull shape variation and morphological systematics of long-nosed armadillos (genus Dasypus)
Background The systematics of long-nosed armadillos (genus Dasypus) has been mainly based on a handful of external morphological characters and classical measurements. Here, we studied the pattern of morphological variation in the skull of long-nosed armadillos species, with a focus on the systematics of the widely distributed nine-banded armadillo (Dasypus novemcinctus). Methods We present the first exhaustive 3D comparison of the skull morphology within the genus Dasypus, based on micro-computed tomography. We used geometric morphometric approaches to explore the patterns of the intra- and interspecific morphological variation of the skull with regard to several factors such as taxonomy, geography, allometry, and sexual dimorphism. Results We show that the shape and size of the skull vary greatly among Dasypus species, with Dasypus pilosus representing a clear outlier compared to other long-nosed armadillos. The study of the cranial intraspecific variation in Dasypus novemcinctus evidences clear links to the geographic distribution and argues in favor of a revision of past taxonomic delimitations. Our detailed morphometric comparisons detected previously overlooked morphotypes of nine-banded armadillos, especially a very distinctive unit restricted to the Guiana Shield. Discussion As our results are congruent with recent molecular data and analyses of the structure of paranasal sinuses, we propose that Dasypus novemcinctus should be regarded either as a polytypic species (with three to four subspecies) or as a complex of several distinct species.
Hautier et al. (2017) Beyond the carapace: skull shape variation and morphological systematics of long-nosed armadillos (genus Dasypus). PeerJ 5:e3650 https://doi.org/10.7717/peerj.3650
Taxonomic and chemical assessment of exceptionally abundant rock mine biofilm
Background An exceptionally thick biofilm covers walls of ancient gold and arsenic Złoty Stok mine (Poland) in the apparent absence of organic sources of energy. Methods and Results We have characterized this microbial community using culture-dependent and independent methods. We sequenced amplicons of the 16S rRNA gene obtained using generic primers and additional primers targeted at Archaea and Actinobacteria separately. Also, we have cultured numerous isolates from the biofilm on different media under aerobic and anaerobic conditions. We discovered very high biodiversity, and no single taxonomic group was dominant. The majority of almost 4,000 OTUs were classified above genus level indicating presence of novel species. Elemental analysis, performed using SEM-EDS and X-ray, of biofilm samples showed that carbon, sulphur and oxygen were not evenly distributed in the biofilm and that their presence is highly correlated. However, the distribution of arsenic and iron was more flat, and numerous intrusions of elemental silver and platinum were noted, indicating that microorganisms play a key role in releasing these elements from the rock. Conclusions Altogether, the picture obtained throughout this study shows a very rich, complex and interdependent system of rock biofilm. The chemical heterogeneity of biofilm is a likely explanation as to why this oligotrophic environment is capable of supporting such high microbial diversity.
Tomczyk-Żak et al. (2017) Taxonomic and chemical assessment of exceptionally abundant rock mine biofilm. PeerJ 5:e3635 https://doi.org/10.7717/peerj.3635