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Subterranean estuaries are biogeochemically active coastal sites resulting from the underground mixing of fresh aquifer groundwater and seawater. In these systems, microbial activity can largely transform the chemical elements that may reach the sea through submarine groundwater discharge (SGD), but little is known about the microorganisms thriving in these land‐sea transition zones. We present the first spatially‐resolved characterization of the bacterial assemblages along a coastal aquifer in the NW Mediterranean, considering the entire subsurface salinity gradient. Combining bulk heterotrophic activity measurements, flow cytometry, microscopy and 16S rRNA gene sequencing we find large variations in prokaryotic abundances, cell size, activity and diversity at both the horizontal and vertical scales that reflect the pronounced physicochemical gradients. The parts of the transect most influenced by freshwater were characterized by smaller cells and lower prokaryotic abundances and heterotrophic production, but some activity hotspots were found at deep low‐oxygen saline groundwater sites enriched in nitrite and ammonium. Diverse, heterogeneous and highly endemic communities dominated by Proteobacteria, Patescibacteria, Desulfobacterota and Bacteroidota were observed throughout the aquifer, pointing to clearly differentiated prokaryotic niches across these transition zones and little microbial connectivity between groundwater and Mediterranean seawater habitats. Finally, experimental manipulations unveiled large increases in community heterotrophic activity driven by fast growth of some rare and site‐specific groundwater Proteobacteria. Our results indicate that prokaryotic communities within subterranean estuaries are highly heterogeneous in terms of biomass, activity and diversity, suggesting that their role in transforming nutrients will also vary spatially within these terrestrial–marine transition zones. [ABSTRACT FROM AUTHOR]

Pathogenic variants in the AP4B1 gene lead to a rare form of hereditary spastic paraplegia (HSP) known as SPG47. We report on a patient with a clinical suspicion of complicated HSP of the lower limbs with intellectual disability, as well as a novel homozygous noncanonical splice site variant in the AP4B1 gene, in which the effect on splicing was validated by RNA analysis. We sequenced 152 genes associated with HSP using Next‐Generation Sequencing (NGS). We isolated total RNA from peripheral blood and generated cDNA using reverse transcription‐polymerase chain reaction (RT‐PCR). A region of AP4B1 mRNA was amplified by PCR and the fragments obtained were purified from the agarose gel and sequenced. We found a homozygous variant of uncertain significance in the AP4B1 gene NM_006594.4: c.1511‐6C>G in the proband. Two different AP4B1 mRNA fragments were obtained in the patient and his carrier parents. The shorter fragment was the predominant fragment in the patient and revealed a deletion with skipping of the AP4B1 exon 10. The patient's longer fragment corresponded to an insertion of the last five nucleotides of AP4B1 intron 9. We confirmed that this variant affects the normal splicing of RNA, sustaining the molecular diagnosis of SPG47 in the patient. [ABSTRACT FROM AUTHOR]

Summary: The aerobic anoxygenic phototrophic (AAP) bacteria are common in most marine environments but their global diversity and biogeography remain poorly characterized. Here, we analyzed AAP communities across 113 globally‐distributed surface ocean stations sampled during the Malaspina Expedition in the tropical and subtropical ocean. By means of amplicon sequencing of the pufM gene, a genetic marker for this functional group, we show that AAP communities along the surface ocean were mainly composed of members of the Halieaceae (Gammaproteobacteria), which were adapted to a large range of environmental conditions, and of different clades of the Alphaproteobacteria, which seemed to dominate under particular circumstances, such as in the oligotrophic gyres. AAP taxa were spatially structured within each of the studied oceans, with communities from adjacent stations sharing more taxonomic similarities. AAP communities were composed of a large pool of rare members and several habitat specialists. When compared to the surface ocean prokaryotic and picoeukaryotic communities, it appears that AAP communities display an idiosyncratic global biogeographical pattern, dominated by selection processes and less influenced by dispersal limitation. Our study contributes to the understanding of how AAP communities are distributed in the horizontal dimension and the mechanisms underlying their distribution across the global surface ocean. [ABSTRACT FROM AUTHOR]

In parts of the Baltic Sea, the phytoplankton spring bloom communities, commonly dominated by diatoms, are shifting toward the co‐occurrence of diatoms and dinoflagellates. Although phytoplankton are known to shape the composition and function of associated bacterioplankton communities, the potential bacterial responses to such a decrease of diatoms are unknown. Here we explored the changes in bacterial communities and heterotrophic production during the spring bloom in four consecutive spring blooms across several sub‐basins of the Baltic Sea and related them to changes in environmental variables and in phytoplankton community structure. The taxonomic structure of bacterioplankton assemblages was partially explained by salinity and temperature but also linked to the phytoplankton community. Higher carbon biomass of the diatoms Achnanthes taeniata, Skeletonema marinoi, Thalassiosira levanderi, and Chaetoceros spp. was associated with more diverse bacterial communities dominated by copiotrophic bacteria (Flavobacteriia, Gammaproteobacteria, and Betaproteobacteria) and higher bacterial production. During dinoflagellate dominance, bacterial production was low and bacterial communities were dominated by Alphaproteobacteria, mainly SAR11. Our results suggest that increases in dinoflagellate abundance during the spring bloom will largely affect the structuring and functioning of the associated bacterial communities. This could decrease pelagic remineralization of organic matter and possibly affect the bacterial grazers communities. [ABSTRACT FROM AUTHOR]

Deep ocean microbial communities rely on the organic carbon produced in the sunlit ocean, yet it remains unknown whether surface processes determine the assembly and function of bathypelagic prokaryotes to a larger extent than deep‐sea physicochemical conditions. Here, we explored whether variations in surface phytoplankton assemblages across Atlantic, Pacific and Indian ocean stations can explain structural changes in bathypelagic (ca. 4,000 m) free‐living and particle‐attached prokaryotic communities (characterized through 16S rRNA gene sequencing), as well as changes in prokaryotic activity and dissolved organic matter (DOM) quality. We show that the spatial structuring of prokaryotic communities in the bathypelagic strongly followed variations in the abundances of surface dinoflagellates and ciliates, as well as gradients in surface primary productivity, but were less influenced by bathypelagic physicochemical conditions. Amino acid‐like DOM components in the bathypelagic reflected variations of those components in surface waters, and seemed to control bathypelagic prokaryotic activity. The imprint of surface conditions was more evident in bathypelagic than in shallower mesopelagic (200–1,000 m) communities, suggesting a direct connectivity through fast‐sinking particles that escape mesopelagic transformations. Finally, we identified a pool of endemic deep‐sea prokaryotic taxa (including potentially chemoautotrophic groups) that appear less connected to surface processes than those bathypelagic taxa with a widespread vertical distribution. Our results suggest that surface planktonic communities shape the spatial structure of the bathypelagic microbiome to a larger extent than the local physicochemical environment, likely through determining the nature of the sinking particles and the associated prokaryotes reaching bathypelagic waters. [ABSTRACT FROM AUTHOR]

Aerobic anoxygenic phototrophic (AAP) bacteria are a phylogenetically diverse and ubiquitous group of prokaryotes that use organic matter but can harvest light using bacteriochlorophyll a. Although the factors regulating AAP ecology have long been investigated through field surveys, the few available experimental studies have considered AAPs as a group, thus disregarding the potential differential responses between taxonomically distinct AAP assemblages. Here, we used sequencing of the pufM gene to describe the diversity of AAPs in 10 environmentally distinct temperate lakes, and to investigate the taxonomic responses of AAP communities in these lakes when subjected to similar experimental manipulations of light and predator removal. The studied communities were clearly dominated by Limnohabitans AAP but presented a clear taxonomic segregation between lakes presumably driven by local conditions, which was maintained after experimental manipulations. Predation reduction (but not light exposure) caused significant compositional shifts across most assemblages, but the magnitude of these changes could not be clearly related to changes in bulk AAP abundances or taxonomic richness of AAP assemblages during experiments. Only a few operational taxonomic units, which differed taxonomically between lakes, were found to respond positively during experimental treatments. Our results highlight that different freshwater AAP communities respond differently to similar control mechanisms, highlighting that in‐depth knowledge on AAP diversity is essential to understand the ecology and potential role of these photoheterotrophs. [ABSTRACT FROM AUTHOR]

Summary: Lake methane (CH4) emissions are largely controlled by aerobic methane‐oxidizing bacteria (MOB) which mostly belong to the classes Alpha‐ and Gammaproteobacteria (Alpha‐ and Gamma‐MOB). Despite the known metabolic and ecological differences between the two MOB groups, their main environmental drivers and their relative contribution to CH4 oxidation rates across lakes remain unknown. Here, we quantified the two MOB groups through CARD‐FISH along the water column of six temperate lakes and during incubations in which we measured ambient CH4 oxidation rates. We found a clear niche separation of Alpha‐ and Gamma‐MOB across lake water columns, which is mostly driven by oxygen concentration. Gamma‐MOB appears to dominate methanotrophy throughout the water column, but Alpha‐MOB may also be an important player particularly in well‐oxygenated bottom waters. The inclusion of Gamma‐MOB cell abundance improved environmental models of CH4 oxidation rate, explaining part of the variation that could not be explained by environmental factors alone. Altogether, our results show that MOB composition is linked to CH4 oxidation rates in lakes and that information on the MOB community can help predict CH4 oxidation rates and thus emissions from lakes. [ABSTRACT FROM AUTHOR]

Aerobic methanotrophic bacteria (methanotrophs) use methane as a source of carbon and energy, thereby mitigating net methane emissions from natural sources. Methanotrophs represent a widespread and phylogenetically complex guild, yet the biogeography of this functional group and the factors that explain the taxonomic structure of the methanotrophic assemblage are still poorly understood. Here, we used high‐throughput sequencing of the 16S rRNA gene of the bacterial community to study the methanotrophic community composition and the environmental factors that influence their distribution and relative abundance in a wide range of freshwater habitats, including lakes, streams and rivers across the boreal landscape. Within one region, soil and soil water samples were additionally taken from the surrounding watersheds in order to cover the full terrestrial–aquatic continuum. The composition of methanotrophic communities across the boreal landscape showed only a modest degree of regional differentiation but a strong structuring along the hydrologic continuum from soil to lake communities, regardless of regions. This pattern along the hydrologic continuum was mostly explained by a clear niche differentiation between type I and type II methanotrophs along environmental gradients in pH, and methane concentrations. Our results suggest very different roles of type I and type II methanotrophs within inland waters, the latter likely having a terrestrial source and reflecting passive transport and dilution along the aquatic networks, but this is an unresolved issue that requires further investigation. [ABSTRACT FROM AUTHOR]

Microbial taxa range from being ubiquitous and abundant across space to extremely rare and endemic, depending on their ecophysiology and on different processes acting locally or regionally. However, little is known about how cosmopolitan or rare taxa combine to constitute communities and whether environmental variations promote changes in their relative abundances. Here we identified the Spatial Abundance Distribution (SpAD) of individual prokaryotic taxa (16S rDNA‐defined Operational Taxonomic Units, OTUs) across 108 globally‐distributed surface ocean stations. We grouped taxa based on their SpAD shape ("normal‐like"‐ abundant and ubiquitous; "logistic"‐ globally rare, present in few sites; and "bimodal"‐ abundant only in certain oceanic regions), and investigated how the abundance of these three categories relates to environmental gradients. Most surface assemblages were numerically dominated by a few cosmopolitan "normal‐like" OTUs, yet there was a gradual shift towards assemblages dominated by "logistic" taxa in specific areas with productivity and temperature differing the most from the average conditions in the sampled stations. When we performed the SpAD categorization including additional habitats (deeper layers and particles of varying sizes), the SpAD of many OTUs changed towards fewer "normal‐like" shapes, and OTUs categorized as globally rare in the surface ocean became abundant. This suggests that understanding the mechanisms behind microbial rarity and dominance requires expanding the context of study beyond local communities and single habitats. We show that marine bacterial communities comprise taxa displaying a continuum of SpADs, and that variations in their abundances can be linked to habitat transitions or barriers that delimit the distribution of community members. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Aim The need to go beyond taxonomy to understand patterns in microbial function has led to an increased use of trait-based approaches, yet we know little about how microbial functional traits vary across large-scale environmental gradients in natural ecosystems. Here, we apply a trait-based approach to explore the large-scale variability in the trait structure underlying the processing of dissolved organic matter (DOM) by boreal bacterioplankton communities, as well as its regulation and links to taxonomic composition. Location Samples were collected from 296 rivers and lakes across five regions in northern Quebec (Canada), which span large gradients in environmental, climatic and geographical properties typical of the boreal zone. Methods We used the metabolic profiles obtained with Biolog EcoPlates® as an imprint of the trait structure underlying bacterial processing of DOM, and Illumina sequencing of the 16SrRNA gene to characterize the taxonomic composition of these bacterial assemblages. The resulting spatial patterns were compared with an array of climatic, landscape and limnological properties varying at the landscape scale. Results Despite a clear regional segregation of the sampled sites based on environmental variables, the trait structure of boreal bacteria did not show any regional or ecosystem-specific patterns, but rather was linked to a gradient of quality of DOM. Community trait configurations diverged progressively with decreasing terrestrial influence, probably due to local processes that transform and diversify the available pool of DOM. This DOM quality gradient did not explain the taxonomic biogeography of these communities, which was controlled by a different set of environmental factors. Main conclusions The functional biogeography of boreal bacterioplankton is driven by the nature of the DOM pool, and particularly by the influence of terrestrial DOM. The lack of coherence between functional and taxonomic biogeographies implies that the environmental controls of freshwater bacterial performance cannot be directly inferred from spatial patterns in taxonomic composition. [ABSTRACT FROM AUTHOR]

Bacteria inhabiting boreal freshwaters are part of metacommunities where local assemblages are often linked by the flow of water in the landscape, yet the resulting spatial structure and the boundaries of the network metacommunity have never been explored. Here, we reconstruct the spatial structure of the bacterial metacommunity in a complex boreal aquatic network by determining the taxonomic composition of bacterial communities along the entire terrestrial/aquatic continuum, including soil and soilwaters, headwater streams, large rivers and lakes. We show that the network metacommunity has a directional spatial structure driven by a common terrestrial origin of aquatic communities, which are numerically dominated by taxa recruited from soils. Local community assembly is driven by variations along the hydrological continuum in the balance between mass effects and species sorting of terrestrial taxa, and seems further influenced by priority effects related to the spatial sequence of entry of soil bacteria into the network. [ABSTRACT FROM AUTHOR]

Catalysed reporter deposition-fluorescence in situ hybridization ( CARD-FISH) is a powerful approach to quantify bacterial taxa. In this study, we compare the performance of the widely used B acteroidetes CF319 a probe with the new CF968 probe. In silico analyses and tests with isolates demonstrate that CF319 a hybridizes with non- B acteroidetes sequences from the R hodobacteraceae and A lteromonadaceae families. We test the probes' accuracy in 37 globally distributed marine samples and over two consecutive years at the Blanes Bay Microbial Observatory ( NW Mediterranean). We also compared the CARD-FISH data with the B acteroidetes 16 S rRNA gene sequences retrieved from 27 marine metagenomes from the TARA Oceans expedition. We find no significant differences in abundances between both approaches, although CF319 a targeted some unspecific sequences and both probes displayed different abundances of specific B acteroidetes phylotypes. Our results demonstrate that quantitative estimations by using both probes are significantly different in certain oceanographic regions ( Mediterranean Sea, Red Sea and Arabian Sea) and that CF968 shows seasonality within marine B acteroidetes, notably large differences between summer and winter that is overlooked by CF319 a. We propose CF968 as an alternative to CF319 a for targeting the whole B acteroidetes phylum since it has better coverage, greater specificity and overall better quantifies marine B acteroidetes. [ABSTRACT FROM AUTHOR]

Dimethylsulfide (DMS) is a biogenic gas with potential climatic effects, and its marine emission depends on the interplay between microbial activity and physical forcing in the oceanic upper mixed layer. We investigated the diel cycling patterns of DMS and its precursor dimethylsulfoniopropionate (DMSP) in four experiments (28 to 48 h long) performed in mesotrophic to ultraoligotrophic Mediterranean and Sargasso Sea waters. Samples taken every 4 or 6 h were analyzed for dimethylated sulfur pools and incubated to measure DMS and DMSP cycling rates, as well as primary and bacterial production. In all four experiments, DMS budgets showed pronounced day versus night variability. In the three summer experiments, gross community DMS production (GPDMS) increased by twofold to threefold from nighttime to daytime, peaking 0-4 h after solar noon. This excess GPDMS was balanced by higher photochemical and microbial sinks during the day, effectively buffering DMS concentrations. In the only winter experiment, GPDMS exhibited opposed temporal dynamics and peaked at nighttime in parallel to total DMSP consumption. Community DMSP to DMS conversion yields were generally <10% throughout the winter experiment and at night in summer, and increased to >15% (even >50%) during the day in summer, presumably due to phytoplankton radiative stress. Our data suggest that (1) diel variability should be taken into account in process studies, diagnostic, and prognostic models of DMS cycling and (2) the community DMS yield is a key variable that defines characteristic DMS cycling regimes. [ABSTRACT FROM AUTHOR]

We investigated the short-term effects of variable solar irradiance and spectrum on the gross biological production of dimethylsulfide (DMS), a trace gas with potential climatic effects, in eight experiments performed at different times of the year in a northwest Mediterranean coastal site. Experimentally determined net community DMS production, DMS photolysis, and dark microbial DMS consumption rates were used to calculate gross community DMS production by budgeting. In addition, the composition of the bacterioplankton and phytoplankton communities in the initial samples, and the photoinhibition of bulk bacterial heterotrophic activity and phytoplankton photosynthetic efficiency were monitored. Our results show that: (1) gross DMS production is irradiance dependent, with a maximum short-term stimulation factor of 2- to 6-fold compared to dark incubations; (2) its spectral shape is variable but generally similar to that of phytoplankton photoinhibition or photodamage, with more effective stimulation at shorter ultraviolet wavelengths; and (3) stronger stimulation occurs when samples are overexposed with respect to their prior exposure. Remarkably, the photoresponse of gross DMS production was in most cases strong enough to (at least) compensate the photochemical DMS loss at the water subsurface. Such response would prevent DMS depletion in stratified and highly irradiated waters. Since the initial microbial communities were representative of meso- to oligotrophic conditions, our observations should apply to a wide variety of oceanic regimes. [ABSTRACT FROM AUTHOR]

The effect of photosynthetically available radiation (PAR; 400-700 nm) and ultraviolet radiation (UVR; 280-400 nm) on marine bacterial heterotrophic activity was assessed monthly throughout a seasonal cycle in Blanes Bay (northwestern Mediterranean Sea). Seawater samples amended with ³H-leucine were exposed to solar radiation under three radiation treatments: PAR +UVR (280-700 nm), PAR +UVA (320-700 nm), and PAR only. Parallel reference incubations in the dark and under a fixed artificial light source (PAR only) were also performed. Exposure to high UVR doses caused strong inhibition of ³H-leucine incorporation rates (LIR), whereas natural PAR doses did not cause overall significant effects. Within UVR, UVA radiation accounted for most of the reduction in LIR, and this effect was modulated by the proportionality of the experimental light to the previous light exposure history of the samples. Constant (artificial) PAR-only exposure led to a general but seasonally variable increase in bacterial heterotrophic production compared to the dark controls, with large increases in spring and lower changes during summer. This pattern was likely caused by the stimulation of the bacterial group Gammaproteobacteria, which showed higher numbers of cells active in ³Hleucine uptake after light exposure. Again, the previous light history of the samples seemed to partly explain the measured effects. Overall, our results show variable responses of bacterial activities to light manipulations, depending on seasonally changing light conditions and communities, and stress the importance of realistic simulation of light exposure conditions for ecosystem-relevant photobiological studies with microbial plankton. [ABSTRACT FROM AUTHOR]

The structural and dynamical changes occurring before nucleotide addition were studied using molecular dynamics (MD) simulations of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) complexes containing one or two Mg2+ ions in the presence of dNTP. Our models revealed that the formation of a catalytically competent DNA polymerase complex required subtle rearrangements at the catalytic site A, which occurred only when an Mg2+ ion was bound. This model has been validated using pre-steady-state kinetics to show that free Mg2+ is necessary to obtain a catalytically competent polymerase. Kinetic studies carried out with Be2+ as a cofactor permitted the functional discrimination between metal sites A and B. At low concentrations, Be2+ increased the catalytic efficiency of the polymerase, while at higher concentrations, it competed with Mg2+ for binding to site A, and inhibited DNA polymerization. In agreement with experimental data, MD simulations revealed that the catalytic attack distance between the 3′-OH of the primer and the α phosphorus in complexes containing Be2+ instead of Mg2+ at site A was above 4.5 Å. Our findings provide a detailed description of the mechanism of DNA polymerization and should be helpful to understand the molecular basis of DNA replication fidelity. Proteins 2008. © 2007 Wiley-Liss, Inc. [ABSTRACT FROM AUTHOR]

We studied leucine turnover using a primed infusion of [1-14C]- l-leucine and glucose turnover using a primed infusion of [6-3H]- d-glucose in five alcoholic patients without liver damage and five age-matched controls. Infusions were maintained for 6 hr, and at the end of the 3rd hour, a 0.8 g/kg iv ethanol load was administered in 20 min. Leucine flux, nonoxidative disposal and oxidation rates, and glucose rate of appearance were calculated during the 3rd and 6th hours of infusion. Ethanol disappearance rate and the percentage completely metabolized to CO2 and H2O in 3 hr were also calculated. Compared with controls, alcoholics had significantly higher basal leucine flux (55.6 ± 12 vs. 37.3 ± 9.3 μ m/m2/min) and nonoxidative disposal (48.7 ± 8.7 vs. 31.1 ± 7.5 μ m/m2/min). No differences were observed in basal glucose appearance rates in alcoholics and controls (397.6 ± 115.2 vs. 349.4 ± 120.6 μ m/m2/min). Compared with controls, alcoholics had a higher alcohol disappearance rate (2.72 ± 0.59 vs. 1.84 ± 0.43 m m/kg/min) and percentage of ethanol metabolized to CO2 and H2O in 3 hr (40.6 ± 10.2 vs. 22.9 ± 6.9%). After the ethanol load, both leucine turnover and glucose rate of appearance decreased significantly only in alcoholics. There was a positive correlation between the change in leucine flux and ethanol disappearance rate and percentage metabolized to CO2 and H2O in alcoholics. [ABSTRACT FROM AUTHOR]

Two diel cycle studies were conducted to determine the effect of day-night light changes on winter bacterial activity in the coastal Mediterranean (Blanes Bay Microbial Observatory). Bacterial abundances, bacterial heterotrophic activity, and flagellate grazing counts were determined at 4-h intervals during two 3-d periods separated by 2 d. Twice a day, the single-cell activity of major bacterial groups was further analyzed by applying microautoradiography combined with catalyzed reporter deposition-fluorescence in situ hybridization. During the first cycle, all the measured parameters (including the number of active cells in most groups) varied synchronously, with higher values at night and lower during the day. An episode of strong winds between the two studied periods disrupted this periodicity at the onset of the second cycle. The bulk incorporation of ³H-leucine recovered the diel pattern after 2 d, mostly driven by the activity of Gammaproteobacteria. Among the possibilities considered, the observed nighttime increases in the grazing activity of heterotrophic nanoflagellates appeared to partially drive the activity of all bacterial taxa through potential periodic release of dissolved organic matter. [ABSTRACT FROM AUTHOR]