The Submarine Volcano Eruption off El Hierro Island: Effects on the Scattering Migrant Biota and the Evolution of the Pelagic Communities

The submarine volcano eruption off El Hierro Island (Canary Islands) on 10 October 2011 promoted dramatic perturbation of the water column leading to changes in the distribution of pelagic fauna. To study the response of the scattering biota, we combined acoustic data with hydrographic profiles and concurrent sea surface turbidity indexes from satellite imagery. We also monitored changes in the plankton and nekton communities through the eruptive and post-eruptive phases. Decrease of oxygen, acidification, rising temperature and deposition of chemicals in shallow waters resulted in a reduction of epipelagic stocks and a disruption of diel vertical migration (nocturnal ascent) of mesopelagic organisms. Furthermore, decreased light levels at depth caused by extinction in the volcanic plume resulted in a significant shallowing of the deep acoustic scattering layer. Once the eruption ceased, the distribution and abundances of the pelagic biota returned to baseline levels. There was no evidence of a volcano-induced bloom in the plankton community.     

Free-Living and Particle-Associated Bacterioplankton in Large Rivers of the Mississippi River Basin Demonstrate Biogeographic Patterns

The different drainage basins of large rivers such as the Mississippi River represent interesting systems in which to study patterns in freshwater microbial biogeography. Spatial variability in bacterioplankton communities in six major rivers (the Upper Mississippi, Missouri, Illinois, Ohio, Tennessee, and Arkansas) of the Mississippi River Basin was characterized using Ion Torrent 16S rRNA amplicon sequencing. When all systems were combined, particle-associated (>3 μm) bacterial assemblages were found to be different from free-living bacterioplankton in terms of overall community structure, partly because of differences in the proportional abundance of sequences affiliated with major bacterial lineages (Alphaproteobacteria, Cyanobacteria, and Planctomycetes). Both particle-associated and free-living communities ordinated by river system, a pattern that was apparent even after rare sequences or those affiliated with Cyanobacteria were removed from the analyses. Ordination of samples by river system correlated with environmental characteristics of each river, such as nutrient status and turbidity. Communities in the Upper Mississippi and the Missouri and in the Ohio and the Tennessee, pairs of rivers that join each other, contained similar taxa in terms of presence-absence data but differed in the proportional abundance of major lineages. The most common sequence types detected in particle-associated communities were picocyanobacteria in the Synechococcus/Prochlorococcus/Cyanobium (Syn/Pro) clade, while free-living communities also contained a high proportion of LD12 (SAR11/Pelagibacter)-like Alphaproteobacteria. This research shows that while different tributaries of large river systems such as the Mississippi River harbor distinct bacterioplankton communities, there is also microhabitat variation such as that between free-living and particle-associated assemblages.     

Nearly a decade‐long repeatable seasonal diversity patterns of bacterioplankton communities in the eutrophic Lake Donghu (Wuhan,China)

Uncovering which environmental factors govern community diversity patterns and how ecological processes drive community turnover are key questions related to understand the community assembly. However, the ecological mechanisms regulating long‐term variations of bacterioplankton communities in lake ecosystems remain poorly understood. Here we present nearly a decade‐long study of bacterioplankton communities from the eutrophic Lake Donghu (Wuhan, China) using 16S rRNA gene amplicon sequencing with MiSeq platform. We found strong repeatable seasonal diversity patterns in terms of both common (detected in more than 50% samples) and dominant (relative abundance >1%) bacterial taxa turnover. Moreover, community composition tracked the seasonal temperature gradient, indicating that temperature is a key environmental factor controlling observed diversity patterns. Total phosphorus also contributed significantly to the seasonal shifts in bacterioplankton composition. However, any spatial pattern of bacterioplankton communities across the main lake areas within season was overwhelmed by their temporal variabilities. Phylogenetic analysis further indicated that 75%–82% of community turnover was governed by homogeneous selection due to consistent environmental conditions within seasons, suggesting that the microbial communities in Lake Donghu are mainly controlled by niche‐based processes. Therefore, dominant niches available within seasons might be occupied by similar combinations of bacterial taxa with modest dispersal rates throughout different lake areas.     

Determining indicator taxa across spatial and seasonal gradients in the Columbia River coastal margin

Bacterioplankton communities are deeply diverse and highly variable across space and time, but several recent studies demonstrate repeatable and predictable patterns in this diversity. We expanded on previous studies by determining patterns of variability in both individual taxa and bacterial communities across coastal environmental gradients. We surveyed bacterioplankton diversity across the Columbia River coastal margin, USA, using amplicon pyrosequencing of 16S rRNA genes from 596 water samples collected from 2007 to 2010. Our results showed seasonal shifts and annual reassembly of bacterioplankton communities in the freshwater-influenced Columbia River, estuary, and plume, and identified indicator taxa, including species from freshwater SAR11, Oceanospirillales, and Flavobacteria groups, that characterize the changing seasonal conditions in these environments. In the river and estuary, Actinobacteria and Betaproteobacteria indicator taxa correlated strongly with seasonal fluctuations in particulate organic carbon (ρ=−0.664) and residence time (ρ=0.512), respectively. In contrast, seasonal change in communities was not detected in the coastal ocean and varied more with the spatial variability of environmental factors including temperature and dissolved oxygen. Indicator taxa of coastal ocean environments included SAR406 and SUP05 taxa from the deep ocean, and Prochlorococcus and SAR11 taxa from the upper water column. We found that in the Columbia River coastal margin, freshwater-influenced environments were consistent and predictable, whereas coastal ocean community variability was difficult to interpret due to complex physical conditions. This study moves beyond beta-diversity patterns to focus on the occurrence of specific taxa and lends insight into the potential ecological roles these taxa have in coastal ocean environments.     

Richness and Diversity of Bacterioplankton Species along an Estuarine Gradient in Moreton Bay, Australia

Bacterioplankton community diversity was investigated in the subtropical Brisbane River-Moreton Bay estuary, Australia (27°25′S, 153°5′E). Bacterial communities were studied using automated rRNA intergenic spacer analysis (ARISA), which amplifies 16S-23S ribosomal DNA internally transcribed spacer regions from mixed-community DNA and detects the separated products on a fragment analyzer. Samples were collected from eight sites throughout the estuary and east to the East Australian Current (Coral Sea). Bacterioplankton communities had the highest operational taxonomic unit (OTU) richness, as measured by ARISA at eastern bay stations (S [total richness] = 84 to 85 OTU) and the lowest richness in the Coral Sea (S = 39 to 59 OTU). Richness correlated positively with bacterial abundance; however, there were no strong correlations between diversity and salinity, NO₃⁻ and PO₄³⁻ concentrations, or chlorophyll a concentration. Bacterioplankton communities at the riverine stations were different from communities in the bay or Coral Sea. The main differences in OTU richness between stations were in taxa that each represented 0.1% (the detection limit) to 0.5% of the total amplified DNA, i.e., the “tail” of the distribution. We found that some bacterioplankton taxa are specific to distinct environments while others have a ubiquitous distribution from river to sea. Bacterioplankton richness and diversity patterns in the estuary are potentially a consequence of greater niche availability, mixing of local and adjacent environment communities, or intermediate disturbance. Furthermore, these results contrast with previous reports of spatially homogeneous bacterioplankton communities in other coastal waters.     

Global patterns of diversity and community structure in marine bacterioplankton

Because of their small size, great abundance and easy dispersal, it is often assumed that marine planktonic microorganisms have a ubiquitous distribution that prevents any structured assembly into local communities. To challenge this view, marine bacterioplankton communities from coastal waters at nine locations distributed world-wide were examined through the use of comprehensive clone libraries of 16S ribosomal RNA genes, used as operational taxonomic units (OTU). Our survey and analyses show that there were marked differences in the composition and richness of OTUs between locations. Remarkably, the global marine bacterioplankton community showed a high degree of endemism, and conversely included few cosmopolitan OTUs. Our data were consistent with a latitudinal gradient of OTU richness. We observed a positive relationship between the relative OTU abundances and their range of occupation, i.e. cosmopolitans had the largest population sizes. Although OTU richness differed among locations, the distributions of the major taxonomic groups represented in the communities were analogous, and all local communities were similarly structured and dominated by a few OTUs showing variable taxonomic affiliations. The observed patterns of OTU richness indicate that similar evolutionary and ecological processes structured the communities. We conclude that marine bacterioplankton share many of the biogeographical and macroecological features of macroscopic organisms. The general processes behind those patterns are likely to be comparable across taxa and major global biomes.     

Particle-size distributions and seasonal diversity of allergenic and pathogenic fungi in outdoor air

Fungi are ubiquitous in outdoor air, and their concentration, aerodynamic diameters and taxonomic composition have potentially important implications for human health. Although exposure to fungal allergens is considered a strong risk factor for asthma prevalence and severity, limitations in tracking fungal diversity in air have thus far prevented a clear understanding of their human pathogenic properties. This study used a cascade impactor for sampling, and quantitative real-time PCR plus 454 pyrosequencing for analysis to investigate seasonal, size-resolved fungal communities in outdoor air in an urban setting in the northeastern United States. From the 20 libraries produced with an average of ∼800 internal transcribed spacer (ITS) sequences (total 15 326 reads), 12 864 and 11 280 sequences were determined to the genus and species levels, respectively, and 558 different genera and 1172 different species were identified, including allergens and infectious pathogens. These analyses revealed strong relationships between fungal aerodynamic diameters and features of taxonomic compositions. The relative abundance of airborne allergenic fungi ranged from 2.8% to 10.7% of total airborne fungal taxa, peaked in the fall, and increased with increasing aerodynamic diameter. Fungi that can cause invasive fungal infections peaked in the spring, comprised 0.1–1.6% of fungal taxa and typically increased in relative abundance with decreasing aerodynamic diameter. Atmospheric fungal ecology is a strong function of aerodynamic diameter, whereby through physical processes, the size influences the diversity of airborne fungi that deposit in human airways and the efficiencies with which specific groups of fungi partition from outdoor air to indoor environments.     

Localized Rejuvenation of a Crystal Mush Recorded in Zircon Temporal and Compositional Variation at the Lassen Volcanic Center,Northern California

Zircon ages and trace element compositions from recent silicic eruptions in the Lassen Volcanic Center (LVC) allow for an evaluation of the timing and conditions of rejuvenation (reheating and mobilization of crystals) within the LVC magmatic system. The LVC is the southernmost active Cascade volcano and, prior to the 1980 eruption of Mount St. Helens, was the site of the only eruption in the Cascade arc during the last century. The three most recent silicic eruptions from the LVC were very small to moderate-sized lava flows and domes of dacite (1915 and 27 ka eruptions of Lassen Peak) and rhyodacite (1.1 ka eruption of Chaos Crags). These eruptions produced mixed and mingled lavas that contain a diverse crystal cargo, including zircon. ²³⁸U-²³⁰Th model ages from interior and surface analyses of zircon reveal ages from ∼17 ka to secular equilibrium (>350 ka), with most zircon crystallizing during a period between ∼60–200 ka. These data support a model for localized rejuvenation of crystal mush beneath the LVC. This crystal mush evidently is the remnant of magmatism that ended ∼190 ka. Most zircon are thought to have been captured from “cold storage” in the crystal mush (670–725°C, Hf >10,000 ppm, Eu/Eu* 0.25–0.4) locally remobilized by intrusion of mafic magma. A smaller population of zircon (>730°C, Hf <10,000 ppm, Eu/Eu* >0.4) grew in, and are captured from, rejuvenation zones. These data suggest the dominant method to produce eruptible melt within the LVC is small-scale, local rejuvenation of the crystal mush accompanied by magma mixing and mingling. Based on zircon stability, the time required to heat, erupt and then cool to background conditions is relatively short, lasting a maximum of 10 s–1000 s years. Rejuvenation events in the LVC are ephemeral and permit eruption within an otherwise waning and cooling magmatic body.     

Incorporating 16S Gene Copy Number Information Improves Estimates of Microbial Diversity and Abundance

The abundance of different SSU rRNA (“16S”) gene sequences in environmental samples is widely used in studies of microbial ecology as a measure of microbial community structure and diversity. However, the genomic copy number of the 16S gene varies greatly – from one in many species to up to 15 in some bacteria and to hundreds in some microbial eukaryotes. As a result of this variation the relative abundance of 16S genes in environmental samples can be attributed both to variation in the relative abundance of different organisms, and to variation in genomic 16S copy number among those organisms. Despite this fact, many studies assume that the abundance of 16S gene sequences is a surrogate measure of the relative abundance of the organisms containing those sequences. Here we present a method that uses data on sequences and genomic copy number of 16S genes along with phylogenetic placement and ancestral state estimation to estimate organismal abundances from environmental DNA sequence data. We use theory and simulations to demonstrate that 16S genomic copy number can be accurately estimated from the short reads typically obtained from high-throughput environmental sequencing of the 16S gene, and that organismal abundances in microbial communities are more strongly correlated with estimated abundances obtained from our method than with gene abundances. We re-analyze several published empirical data sets and demonstrate that the use of gene abundance versus estimated organismal abundance can lead to different inferences about community diversity and structure and the identity of the dominant taxa in microbial communities. Our approach will allow microbial ecologists to make more accurate inferences about microbial diversity and abundance based on 16S sequence data.     

Seasonal microbial community dynamics correlate with phytoplankton-derived polysaccharides in surface coastal waters

Phytoplankton produce large amounts of polysaccharide gel material known as transparent exopolymer particles (TEP). We investigated the potential links between phytoplankton-derived TEP and microbial community structure in the sea surface microlayer and underlying water at the English Channel time-series station L4 during a spring diatom bloom, and in two adjacent estuaries. Major changes in bacterioneuston and bacterioplankton community structure occurred after the peak of the spring bloom at L4, and coincided with the significant decline of microlayer and water column TEP. Increased abundance of Flavobacteriales and Rhodobacterales in bacterioneuston and bacterioplankton communities at L4 was significantly related to the TEP decline, indicating that both taxa could be responsible. The results suggest that TEP is an important factor in determining microbial diversity in coastal waters, and that TEP utilisation could be a niche occupied by Flavobacteriales and Rhodobacterales.     

More,smaller bacteria in response to ocean's warming?

Heterotrophic bacteria play a major role in organic matter cycling in the ocean. Although the high abundances and relatively fast growth rates of coastal surface bacterioplankton make them suitable sentinels of global change, past analyses have largely overlooked this functional group. Here, time series analysis of a decade of monthly observations in temperate Atlantic coastal waters revealed strong seasonal patterns in the abundance, size and biomass of the ubiquitous flow-cytometric groups of low (LNA) and high nucleic acid (HNA) content bacteria. Over this relatively short period, we also found that bacterioplankton cells were significantly smaller, a trend that is consistent with the hypothesized temperature-driven decrease in body size. Although decadal cell shrinking was observed for both groups, it was only LNA cells that were strongly coherent, with ecological theories linking temperature, abundance and individual size on both the seasonal and interannual scale. We explain this finding because, relative to their HNA counterparts, marine LNA bacteria are less diverse, dominated by members of the SAR11 clade. Temperature manipulation experiments in 2012 confirmed a direct effect of warming on bacterial size. Concurrent with rising temperatures in spring, significant decadal trends of increasing standing stocks (3% per year) accompanied by decreasing mean cell size (−1% per year) suggest a major shift in community structure, with a larger contribution of LNA bacteria to total biomass. The increasing prevalence of these typically oligotrophic taxa may severely impact marine food webs and carbon fluxes by an overall decrease in the efficiency of the biological pump.     

Landscape‐scale spatial abundance distributions discriminate core from random components of boreal lake bacterioplankton

Aquatic bacterial communities harbour thousands of coexisting taxa. To meet the challenge of discriminating between a ‘core’ and a sporadically occurring ‘random’ component of these communities, we explored the spatial abundance distribution of individual bacterioplankton taxa across 198 boreal lakes and their associated fluvial networks (188 rivers). We found that all taxa could be grouped into four distinct categories based on model statistical distributions (normal like, bimodal, logistic and lognormal). The distribution patterns across lakes and their associated river networks showed that lake communities are composed of a core of taxa whose distribution appears to be linked to in‐lake environmental sorting (normal‐like and bimodal categories), and a large fraction of mostly rare bacteria (94% of all taxa) whose presence appears to be largely random and linked to downstream transport in aquatic networks (logistic and lognormal categories). These rare taxa are thus likely to reflect species sorting at upstream locations, providing a perspective of the conditions prevailing in entire aquatic networks rather than only in lakes.     

Spatial variability overwhelms seasonal patterns in bacterioplankton communities across a river to ocean gradient

Few studies of microbial biogeography address variability across both multiple habitats and multiple seasons. Here we examine the spatial and temporal variability of bacterioplankton community composition of the Columbia River coastal margin using 16S amplicon pyrosequencing of 300 water samples collected in 2007 and 2008. Communities separated into seven groups (ANOSIM, P<0.001): river, estuary, plume, epipelagic, mesopelagic, shelf bottom (depth<350 m) and slope bottom (depth>850 m). The ordination of these samples was correlated with salinity (ρ=−0.83) and depth (ρ=−0.62). Temporal patterns were obscured by spatial variability among the coastal environments, and could only be detected within individual groups. Thus, structuring environmental factors (for example, salinity, depth) dominate over seasonal changes in determining community composition. Seasonal variability was detected across an annual cycle in the river, estuary and plume where communities separated into two groups, early year (April–July) and late year (August–Nov), demonstrating annual reassembly of communities over time. Determining both the spatial and temporal variability of bacterioplankton communities provides a framework for modeling these communities across environmental gradients from river to deep ocean.     

Bacterial and phytoplankton responses to nutrient amendments in a boreal lake differ according to season and to taxonomic resolution

Nutrient limitation and resource competition in bacterial and phytoplankton communities may appear different when considering different levels of taxonomic resolution. Nutrient amendment experiments conducted in a boreal lake on three occasions during one open water season revealed complex responses in overall bacterioplankton and phytoplankton abundance and biovolume. In general, bacteria were dominant in spring, while phytoplankton was clearly the predominant group in autumn. Seasonal differences in the community composition of bacteria and phytoplankton were mainly related to changes in observed taxa, while the differences across nutrient treatments within an experiment were due to changes in relative contributions of certain higher- and lower-level phylogenetic groups. Of the main bacterioplankton phyla, only Actinobacteria had a treatment response that was visible even at the phylum level throughout the season. With increasing resolution (from 75 to 99% sequence similarity) major responses to nutrient amendments appeared using 454 pyrosequencing data of 16S rRNA amplicons. This further revealed that OTUs (defined by 97% sequence similarity) annotated to the same highly resolved freshwater groups appeared to occur during different seasons and were showing treatment-dependent differentiation, indicating that OTUs within these groups were not ecologically coherent. Similarly, phytoplankton species from the same genera responded differently to nutrient amendments even though biovolumes of the majority of taxa increased when both nitrogen and phosphorus were added simultaneously. The bacterioplankton and phytoplankton community compositions showed concurrent trajectories that could be seen in synchronous succession patterns over the season. Overall, our data revealed that the response of both communities to nutrient changes was highly dependent on season and that contradictory results may be obtained when using different taxonomic resolutions.     

Invasiveness Does Not Predict Impact: Response of Native Land Snail Communities to Plant Invasions in Riparian Habitats

Studies of plant invasions rarely address impacts on molluscs. By comparing pairs of invaded and corresponding uninvaded plots in 96 sites in floodplain forests, we examined effects of four invasive alien plants (Impatiens glandulifera, Fallopia japonica, F. sachalinensis, and F.×bohemica) in the Czech Republic on communities of land snails. The richness and abundance of living land snail species were recorded separately for all species, rare species listed on the national Red List, and small species with shell size below 5 mm. The significant impacts ranged from 16–48% reduction in snail species numbers, and 29–90% reduction in abundance. Small species were especially prone to reduction in species richness by all four invasive plant taxa. Rare snails were also negatively impacted by all plant invaders, both in terms of species richness or abundance. Overall, the impacts on snails were invader-specific, differing among plant taxa. The strong effect of I. glandulifera could be related to the post-invasion decrease in abundance of tall nitrophilous native plant species that are a nutrient-rich food source for snails in riparian habitats. Fallopia sachalinensis had the strongest negative impact of the three knotweeds, which reflects differences in their canopy structure, microhabitat humidity and litter decomposition. The ranking of Fallopia taxa according to the strength of impacts on snail communities differs from ranking by their invasiveness, known from previous studies. This indicates that invasiveness does not simply translate to impacts of invasion and needs to be borne in mind by conservation and management authorities.     

Nematode succession at deep-sea hydrothermal vents after a recent volcanic eruption with the description of two dominant species

Nematodes are very common in the deep sea and are an important component of deep-sea hydrothermal vent communities. In early 2006, the eruption of the underwater volcano at 9°50’N East Pacific Rise wiped out almost the entire faunal communities of the area. This provided us with the opportunity to study nematode primary succession at vents as well as on adjacent seafloor basalt. Nematode abundance and richness were extremely low at all studied sites in late 2006 and 2007, and increased only slightly in 2009. Interestingly, the most abundant species during early succession were also prominent in this area prior to the eruption. Our results show that nematodes are extremely influenced by volcanic eruptions and need a long period of time to colonize the lava-flooded area in greater numbers and richness. We hypothesize that low food availability on the young bare basalt and harsh environmental conditions at early succession vent sites might hinder a more successful nematode establishment. In addition to the newly established active vent sites we also studied an inactive vent site that was not directly hit by the eruption but whose vent fluid had ceased after the eruption. At this inactive and older vent, diversity was also relatively low but was higher than at the younger, newly established sites. In addition to the ecological analyses, we here describe the two most abundant species found at inactive vents, namely Neochromadora aff. poecilosoma De Mann 1893 and Linhomoeus caudipapillosus sp. n.     

Flow-Cytometric Cell Sorting and Subsequent Molecular Analyses for Culture-Independent Identification of Bacterioplankton Involved in Dimethylsulfoniopropionate Transformations

Marine bacterioplankton transform dimethylsulfoniopropionate (DMSP) into the biogeochemically important and climatically active gas dimethylsulfide. In order to identify specific bacterial taxa mediating DMSP processing in a natural marine ecosystem, we amended water samples from a southeastern U.S. salt marsh with 20 μM DMSP and tracked community shifts with flow cytometry (FCM) coupled to 16S rRNA gene analyses. In two out of four seasons studied, DMSP amendments induced the formation of distinct bacterioplankton populations with elevated nucleic acid (NA) content within 24 h, indicative of cells actively utilizing DMSP. The 16S rRNA genes of the cells with and without elevated NA content were analyzed following cell sorting and PCR amplification with sequencing and terminal restriction fragment length polymorphism approaches. Compared to cells in the control FCM populations, bacteria with elevated NA content in the presence of DMSP were relatively enriched in taxa related to Loktanella, Oceanicola, and Sulfitobacter (Roseobacter lineage, α-Proteobacteria); Caulobacter (α-Proteobacteria); and Brachymonas and Xenophilus (β-Proteobacteria) in the May-02 sample and to Ketogulonicigenium (Roseobacter lineage, α-Proteobacteria) and novel γ-Proteobacteria in the Sept-02 sample. Our study suggests that diverse bacterioplankton participate in the metabolism of DMSP in coastal marine systems and that their relative importance varies temporally.     

A comparative study of the cytometric characteristics of high and low nucleic-acid bacterioplankton cells from different aquatic ecosystems

Flow cytometry has revealed the existence of two distinct fractions of bacterioplankton cells, characterized by high and low nucleic acid contents (HNA and LNA cells). Although these fractions seem ubiquitous in aquatic systems, little is known concerning the variation in the cytometric parameters used to characterize them. We have performed cytometric analyses of samples from a wide range of aquatic systems to determine the magnitude and variability in the cytometric characteristics of HNA/LNA. We show that neither group is associated to a fixed level of fluorescence and of light scatter. Rather, the relative position of HNA and LNA in the fluorescence versus side scatter cytograms varies greatly, both within and among ecosystems. Although the cytometric parameters of both groups tend to covary, there is often uncoupling between the two, particularly in light scatter. Our results show that, although the basic HNA/LNA configuration is present in most samples, its cytometric expression changes greatly in different ecosystems and along productivity gradients. The patterns in cytometric parameters do not support the simple, dichotomous view of HNA and LNA as active and inactive cells, or the notion of two distinct and independent communities, but rather suggest that there may be cells that are intrinsic to each fraction, as well as others that may exchange between fractions.