Multivariate analyses in microbial ecology

Environmental microbiology is undergoing a dramatic revolution due to the increasing accumulation of biological information and contextual environmental parameters. This will not only enable a better identification of diversity patterns, but will also shed more light on the associated environmental conditions, spatial locations, and seasonal fluctuations, which could explain such patterns. Complex ecological questions may now be addressed using multivariate statistical analyses, which represent a vast potential of techniques that are still underexploited. Here, well-established exploratory and hypothesis-driven approaches are reviewed, so as to foster their addition to the microbial ecologist toolbox. Because such tools aim at reducing data set complexity, at identifying major patterns and putative causal factors, they will certainly find many applications in microbial ecology

Effects of Eutrophication, Seasonality and Macrofouling on the Diversity of Bacterial Biofilms in Equatorial Coral Reefs

Biofilms play an important role as a settlement cue for invertebrate larvae and significantly contribute to the nutrient turnover in aquatic ecosystems. Nevertheless, little is known about how biofilm community structure generally responds to environmental changes. This study aimed to identify patterns of bacterial dynamics in coral reef biofilms in response to associated macrofouling community structure, microhabitat (exposed vs. sheltered), seasonality, and eutrophication. Settlement tiles were deployed at four reefs along a cross-shelf eutrophication gradient and were exchanged every 4 months over 20 months. The fouling community composition on the tiles was recorded and the bacterial community structure was assessed with the community fingerprinting technique Automated Ribosomal Intergenic Spacer Analysis (ARISA). Bacterial operational taxonomic unit (OTU) number was higher on exposed tiles, where the fouling community was homogenous and algae-dominated, than in sheltered habitats, which were occupied by a variety of filter feeders. Furthermore, OTU number was also highest in eutrophied near-shore reefs, while seasonal variations in community structure were most pronounced in the oligotrophic mid-shelf reef. In contrast, the macrofouling community structure did not change significantly with seasons. Changes in bacterial community patterns were mostly affected by microhabitat, seasonal and anthropogenically derived changes in nutrient availability, and to a lesser extent by changes in the macrofouling community structure. Path analysis revealed a complex interplay of various environmental and biological factors explaining the spatial and temporal variations in bacterial biofilm communities under natural conditions

Repeatedly Evolved Host-Specific Ectosymbioses between Sulfur-Oxidizing Bacteria and Amphipods Living in a Cave Ecosystem

Ectosymbioses between invertebrates and sulfur-oxidizing bacteria are widespread in sulfidic marine environments and have evolved independently in several invertebrate phyla. The first example from a freshwater habitat, involving Niphargus ictus amphipods and filamentous Thiothrix ectosymbionts, was recently reported from the sulfide-rich Frasassi caves in Italy. Subsequently, two new Niphargus species, N. frasassianus and N. montanarius, were discovered within Frasassi and found to co-occur with N. ictus. Using a variety of microscopic and molecular techniques, we found that all three Frasassi-dwelling Niphargus species harbor Thiothrix ectosymbionts, which belong to three distinct phylogenetic clades (named T1, T2, and T3). T1 and T3 Thiothrix dominate the N. frasassianus ectosymbiont community, whereas T2 and T3 are prevalent on N. ictus and N. montanarius. Relative distribution patterns of the three ectosymbionts are host species-specific and consistent over different sampling locations and collection years. Free-living counterparts of T1–T3 are rare or absent in Frasassi cave microbial mats, suggesting that ectosymbiont transmission among Niphargus occurs primarily through inter- or intraspecific inoculations. Phylogenetic analyses indicate that the Niphargus-Thiothrix association has evolved independently at least two times. While ectosymbioses with T1 and T2 may have been established within Frasassi, T3 ectosymbionts seem to have been introduced to the cave system by Niphargus

CO₂ leakage can cause loss of benthic biodiversity in submarine sands

One of the options to mitigate atmospheric CO2 increase is CO2 Capture and Storage in sub-seabed geological formations. Since predicting long-term storage security is difficult, different CO2 leakage scenarios and impacts on marine ecosystems require evaluation. Submarine CO2 vents may serve as natural analogues and allow studying the effects of CO2 leakage in a holistic approach. At the study site east of Basiluzzo Islet off Panarea Island (Italy), gas emissions (90–99% CO2) occur at moderate flows (80–120 L m−2 h−1). We investigated the effects of acidified porewater conditions (pHT range: 5.5–7.7) on the diversity of benthic bacteria and invertebrates by sampling natural sediments in three subsequent years and by performing a transplantation experiment with a duration of one year, respectively. Both multiple years and one year of exposure to acidified porewater conditions reduced the number of benthic bacterial operational taxonomic units and invertebrate species diversity by 30–80%. Reduced biodiversity at the vent sites increased the temporal variability in bacterial and nematode community biomass, abundance and composition. While the release from CO2 exposure resulted in a full recovery of nematode species diversity within one year, bacterial diversity remained affected. Overall our findings showed that seawater acidification, induced by seafloor CO2 emissions, was responsible for loss of diversity across different size-classes of benthic organisms, which reduced community stability with potential relapses on ecosystem resilience

Prevalence of carbapenem-resistant Acinetobacter baumannii from 2005 to 2016 in Switzerland

Background : We describe the prevalence of invasive carbapenem-resistant Acinetobacter spp. isolated from 2005 to 2016 in different regions of Switzerland.Methods: Using the Swiss Antibiotic Resistance Centre (anresis) database that includes data from 70% of all hospitalized patients and one third of all ambulatory practitioners in Switzerland, we analysed the number of carbapenem- susceptible and resistant Acinetobacter spp. isolated from blood or cerebrospinal fluid, and further described their temporal and regional fluctuations.Results: From 2005 to 2016, 58 cases of resistant or intermediate strains to carbapenem were observed among 632 cases of invasive Acinetobacter. Multivariable analyses indicated that the number of carbapenem-resistant isolates (mean 4.8 ± sd 2.12) and carbapenem resistance rates per region per annum (8.4% ± 13.9%) were low and stable over the studied period. Large fluctuations were observed at the regional level, with e.g. the North East region displaying resistance rates twice as high as that found in other regions.Conclusion: Despite a relatively stable number of carbapenem-resistant Acinetobacter isolates in Switzerland, our results suggest the existence of a diverse pool of A. baumannii species in hospital settings, and confirm the implication of carbapenem-resistant Acinetobacter calcoaceticus-Acinetobacter baumannii (ACB) complex in the vast majority of clinical infections and nosocomial outbreaks with notable regional fluctuations

Microbial habitat connectivity across spatial scales and hydrothermal temperature gradients at Guaymas Basin

The Guaymas Basin (Gulf of California) hydrothermal vent area is known as a dynamic and hydrothermally vented sedimentary system, where the advection and production of a variety of different metabolic substrates support a high microbial diversity and activity in the seafloor. The main objective of our study was to explore the role of temperature and other environmental factors on community diversity, such as the presence of microbial mats and seafloor bathymetry within one hydrothermally vented field of 200 x 250 m dimension. In this field, temperature increased strongly with sediment depth reaching the known limit of life within a few decimeters. Potential sulfate reduction rate as a key community activity parameter was strongly affected by in situ temperature and sediment depth, declining from high rates of 1-5 jimol m1-1 d-1 at the surface to the detection limit below 5 cm sediment depth, despite the presence of sulfate and hydrocarbons. Automated Ribosomal lntergenic Spacer Analysis yielded a high-resolution fingerprint of the dominant members of the bacterial community. Our analyses showed strong temperature and sediment depth effects on bacterial cell abundance and Operational Taxonomic Units (OTUs) number, both declining by more than one order of magnitude below the top 5 cm of the sediment surface. Another fraction of the variation in diversity and community structure was explained by differences in the local bathymetry and spatial position within the vent field. Nevertheless, more than 80% of all detected OTUs were shared among the different temperature realms and sediment depths, after being classified as cold (T 40 C) temperature conditions, with significant OTU overlap with the richer surface communities. Overall, this indicates a high connectivity of benthic bacterial habitats in this dynamic and heterogeneous marine ecosystem influenced by strong hydrothermalism

Epidemiology of human adenoviruses: a 20-year retrospective observational study in hospitalized patients in Bern, Switzerland.

Background: Human adenovirus (HAdV) is an important pathogen seen in clinical practice. Long-term studies may help better understand epidemiological trends and changes in circulating genotypes over time. Purpose: Using a large biobank of samples from hospitalized, adenovirus-positive patients over a 20-year period, we aimed to analyze long-term epidemiological trends and genotypic relatedness among circulating HAdV strains. Methods: Based on samples from hospitalized patients confirmed to be HAdV positive in Bern, Switzerland, from 1998 to 2017, and on their associated demographic and clinical data, we identified epidemiological trends and risk factors associated with HAdV infection. HAdV genotyping was performed by PCR amplification and sequencing of the hypervariable hexon gene. The obtained sequences were phylogenetically compared with sequences from international HAdV strains. Results: HAdV was identified in 1302 samples tested. Cases of HAdV infection were reported throughout the years with no clear seasonality. Upper respiratory tract samples, conjunctivitis swabs, and stool had the highest positivity rate (56.2%, 18.7%, and 14.2% of the cases, respectively). HAdV infection was highest among children ≤4 years old. Increased number of HAdV cases were observed in years 2009 (n = 110) and 2010 (n =112). HAdV8 was the predominant genotype among patients older than 20 years, and was mostly associated with ophthalmic infection. Predominant genotypes among children ≤4 years old were HAdV1, HAdV2, and HAdV3, which were mostly associated with respiratory tract infections. Recurring peaks of increased HAdV cases were evidenced every 4 years among children ≤4 years old. Conclusion: Our study gives novel insights on long-term epidemiological trends and phylogenetic relatedness among circulating HAdV strains in Switzerland, country in which little data on HAdV prevalence and diversity was so far available

Spatial patterns and links between microbial community composition and function in cyanobacterial mats

We imaged reflectance and variable fluorescence in 25 cyanobacterial mats from four distant sites around the globe to assess, at different scales of resolution, spatial variabilities in the physiological parameters characterizing their photosynthetic capacity, including the absorptivity by chlorophyll a (Achl), maximum quantum yield of photosynthesis (Ymax), and light acclimation irradiance (Ik). Generally, these parameters significantly varied within individual mats on a sub-millimeter scale, with about 2-fold higher variability in the vertical than in the horizontal direction. The average vertical profiles of Ymax and Ik decreased with depth in the mat, while Achl exhibited a sub-surface maximum. The within-mat variability was comparable to, but often larger than, the between-sites variability, whereas the within-site variabilities (i.e., between samples from the same site) were generally lowest. When compared based on averaged values of their photosynthetic parameters, mats clustered according to their site of origin. Similar clustering was found when the community composition of the mats' cyanobacterial layers were compared by automated ribosomal intergenic spacer analysis (ARISA), indicating a significant link between the microbial community composition and function. Although this link is likely the result of community adaptation to the prevailing site-specific environmental conditions, our present data is insufficient to identify the main factors determining these patterns. Nevertheless, this study demonstrates that the spatial variability in the photosynthetic capacity and light acclimation of benthic phototrophic microbial communities is at least as large on a sub-millimeter scale as it is on a global scale, and suggests that this pattern of variability scaling is similar for the microbial community composition. © 2014 Al-Najjar, Ramette, Kühl, Hamza, Klatt and Polerecky

Landau-Forbidden Quantum Criticality in Rydberg Quantum Simulators

The Landau-Ginzburg-Wilson theory of phase transitions precludes a continuous transition between two phases that spontaneously break distinct symmetries. However, quantum mechanical effects can intertwine the symmetries, giving rise to an exotic phenomenon called deconfined quantum criticality (DQC). In this work, we study the ground state phase diagram of a one-dimensional array of individually trapped neutral atoms interacting strongly via Rydberg states, and demonstrate through extensive numerical simulations that it hosts a variety of symmetry-breaking phases and their transitions including DQC. We show how an enlarged, emergent continuous symmetry arises at the DQCs, which can be experimentally observed in the joint distribution of two distinct order parameters, obtained within measurement snapshots in the standard computational basis. Our findings highlight quantum simulators of Rydberg atoms not only as promising platforms to experimentally realize such exotic phenomena, but also as unique ones allowing access to physical properties not obtainable in traditional experiments

Pseudomonas protegens sp. nov., widespread plant-protecting bacteria producing the biocontrol compounds 2,4-diacetylphloroglucinol and pyoluteorin

Fluorescent Pseudomonas strains producing the antimicrobial secondary metabolite 2,4-diacetylphloroglucinol (Phl) play a prominent role in the biocontrol of plant diseases. A subset of Phl-producing fluorescent Pseudomonas strains, which can additionally synthesize the antimicrobial compound pyoluteorin (Plt), appears to cluster separately from other fluorescent Pseudomonas spp. based on 16S rRNA gene analysis and shares at most 98.4% 16S rRNA gene sequence identity with any other Pseudomonas species. In this study, a polyphasic approach based on molecular and phenotypic methods was used to clarify the taxonomy of representative Phl+ Plt+ strains isolated from tobacco, cotton or wheat on different continents. Phl+ Plt+ strains clustered separately from their nearest phylogenetic neighbors (i.e. species from the ‘P. syringae’, ‘P. fluorescens’ and ‘P. chlororaphis’ species complexes) based on rpoB, rpoD or gyrB phylogenies. DNA-DNA hybridization experiments clarified that Phl+ Plt+ strains formed a tight genomospecies that was distinct from P. syringae, P. fluorescens, or P. chlororaphis type strains. Within Phl+ strains, the Phl+ Plt+ strains were differentiated from other biocontrol fluorescent Pseudomonas strains that produced Phl but not Plt, based on phenotypic and molecular data. Discriminative phenotypic characters were also identified by numerical taxonomic analysis and siderotyping. Altogether, this polyphasic approach supported the conclusion that Phl+ Plt+ fluorescent Pseudomonas strains belonged to a novel species for which the name Pseudomonas protegens is proposed, with CHA0T (=CFBP 6595T, =DSM 19095T) as the type strain