Primer selection impacts specific population abundances but not community dynamics in a monthly time-series 16S rRNA gene amplicon analysis of coastal marine bacterioplankton.

Primers targeting the 16S small subunit ribosomal RNA marker gene, used to characterize bacterial and archaeal communities, have recently been re-evaluated for marine planktonic habitats. To investigate whether primer selection affects the ecological interpretation of bacterioplankton populations and community dynamics, amplicon sequencing with four primer sets targeting several hypervariable regions of the 16S rRNA gene was conducted on both mock communities constructed from cloned 16S rRNA genes and a time-series of DNA samples from the temperate coastal Santa Barbara Channel. Ecological interpretations of community structure (delineation of depth and seasonality, correlations with environmental factors) were similar across primer sets, while population dynamics varied. We observed substantial differences in relative abundances of taxa known to be poorly resolved by some primer sets, such as Thaumarchaeota and SAR11, and unexpected taxa including Roseobacter clades. Though the magnitude of relative abundances of common OTUs differed between primer sets, the relative abundances of the OTUs were nonetheless strongly correlated. We do not endorse one primer set but rather enumerate strengths and weaknesses to facilitate selection appropriate to a system or experimental goal. While 16S rRNA gene primer bias suggests caution in assessing quantitative population dynamics, community dynamics appear robust across studies using different primers

Contrasting prefrontal cortex contributions to episodic memory dysfunction in behavioural variant frontotemporal dementia and alzheimer's disease

Recent evidence has questioned the integrity of episodic memory in behavioural variant frontotemporal dementia (bvFTD), where recall performance is impaired to the same extent as in Alzheimer's disease (AD). While these deficits appear to be mediated by divergent patterns of brain atrophy, there is evidence to suggest that certain prefrontal regions are implicated across both patient groups. In this study we sought to further elucidate the dorsolateral (DLPFC) and ventromedial (VMPFC) prefrontal contributions to episodic memory impairment in bvFTD and AD. Performance on episodic memory tasks and neuropsychological measures typically tapping into either DLPFC or VMPFC functions was assessed in 22 bvFTD, 32 AD patients and 35 age- and education-matched controls. Behaviourally, patient groups did not differ on measures of episodic memory recall or DLPFC-mediated executive functions. BvFTD patients were significantly more impaired on measures of VMPFC-mediated executive functions. Composite measures of the recall, DLPFC and VMPFC task scores were covaried against the T1 MRI scans of all participants to identify regions of atrophy correlating with performance on these tasks. Imaging analysis showed that impaired recall performance is associated with divergent patterns of PFC atrophy in bvFTD and AD. Whereas in bvFTD, PFC atrophy covariates for recall encompassed both DLPFC and VMPFC regions, only the DLPFC was implicated in AD. Our results suggest that episodic memory deficits in bvFTD and AD are underpinned by divergent prefrontal mechanisms. Moreover, we argue that these differences are not adequately captured by existing neuropsychological measures

Draft genome sequence of marine alphaproteobacterial strain HIMB11, the first cultivated representative of a unique lineage within the Roseobacter clade possessing an unusually small genome

© The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Standards in Genomic Sciences 9 (2014): 632-645, doi:10.4056/sigs.4998989.Strain HIMB11 is a planktonic marine bacterium isolated from coastal seawater in Kaneohe Bay, Oahu, Hawaii belonging to the ubiquitous and versatile Roseobacter clade of the alphaproteobacterial family Rhodobacteraceae. Here we describe the preliminary characteristics of strain HIMB11, including annotation of the draft genome sequence and comparative genomic analysis with other members of the Roseobacter lineage. The 3,098,747 bp draft genome is arranged in 34 contigs and contains 3,183 protein-coding genes and 54 RNA genes. Phylogenomic and 16S rRNA gene analyses indicate that HIMB11 represents a unique sublineage within the Roseobacter clade. Comparison with other publicly available genome sequences from members of the Roseobacter lineage reveals that strain HIMB11 has the genomic potential to utilize a wide variety of energy sources (e.g. organic matter, reduced inorganic sulfur, light, carbon monoxide), while possessing a reduced number of substrate transporters.We gratefully acknowledge the support of the Gordon and Betty Moore Foundation, which funded the sequencing of this genome. Annotation was performed as part of the 2011 C-MORE Summer Course in Microbial Oceanography (http://cmore.soest.hawaii.edu/summercourse/2011/index.htm), with support by the Agouron Institute, the Gordon and Betty Moore Foundation, the University of Hawaii and Manoa School of Ocean and Earth Science and Technology (SOEST), and the Center for Microbial Oceanography: Research and Education (C-MORE), a National Science Foundation-funded Science and Technology Center (award No. EF0424599)

Effects of Inter-tributary Dissolved Organic Carbon Variability on Heterotrophic Microbial Communities in Upper Winyah Bay, SC

Winyah Bay, SC, is a riverine-dominated estuary whose four main blackwater tributaries enter the estuary within eight kilometers of one another. These rivers\u27 differing watershed land use patterns allow for comparisons of bacterial activity and carbon properties under different allochthonous loading regimes. This study examined dissolved organic carbon (DOC), characterized by concentration, lability as measured by 21-day consumption bioassays, and UV-Visible absorption spectra; bacterial community composition based on terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rDNA; community metabolic diversity as measured by Biolog GN2 plates; and associated nutrient and in situ data. Strong seasonal shifts were observed in DOC concentration, measures of DOC quality, and corollary factors, while DOC lability appeared to be impacted by discrete events. In situ DOC concentrations were measured between 475 and 2000 µmol/1 in the rivers and 550 to 1100 µmol/1 in the Bay. Between 1.9 and 11.9% of total DOC was consumed in the bioassays, and consumption was independent of in situ DOC concentrations. While lability differed significantly by date, it was not significant between sites. Lability in the system as a whole was best explained by in situ pH, chlorophyll a, and carbon-specific a355, while explanatory factors of lability differed across individual sites. Biolog plates indicated significant differences in community metabolic activity between sites and dates, although these were to strongly correlated with environmental or carbon variables. Gini coefficients, a measure of the metabolic diversity of a community, showed that sites with greater carbon lability also had more metabolically diverse communities. T-RFLP analysis showed significant differences in phylogenetic community structure between sites and dates, with several carbon and environmental factors relating to these differences. T-RFLP communities were positively correlated with environmental variables excluding carbon but not including carbon, possibly due to a reduced data set. Metabolic community structure as measured by Biolog plates, however, was never significantly correlated with environmental variables. T-RFLP and Biolog measures of community structure were positively correlated both on their own and after correcting for environmental variables. This study did not support the overall hypothesis that land use on the watershed scale would drive carbon lability. However, it suggests that carbon lability may be achieve relatively equivalent values in neighboring systems, despite the probability that lability in each of those systems is being driven by a different suite of mechanisms. Additionally, both phylogenetic structure and community metabolic diversity were significantly related to carbon lability. Finally, the significant correlation between T-RFLP and Biolog measures of community structure further supports the paradigm that phylogeny and catabolic genes are, at the least, loosely related

Flow cytometric abundances in Flathead Lake, Montana

Three years of both non-pigmented and cyanobacteria cellular abundances in temperate, oligotrophic Flathead Lake, recorded on an Attune Accoustic Focusing flow cytometer. Lake water was collected from Flathead Lake's main sampling location 'Midlake Deep' (47° 52´ N, 114° 4´ W) at 5 depths (5 m, 10 m, 50 m, 90 m, and the depth-variable chlorophyll maximum). Data presented in: Evans, K. A., L. M. Peoples, J. R. Ranieri, E. K. Wear, and M. J. Church. 2023. Mixing-driven changes in distributions and abundances of planktonic microorganisms in Flathead Lake

Draft genome sequence of marine alphaproteobacterial strain HIMB11, the first cultivated representative of a unique lineage within the \u3cem\u3eRoseobacter\u3c/em\u3e clade possessing an unusually small genome

Strain HIMB11 is a planktonic marine bacterium isolated from coastal seawater in Kaneohe Bay, Oahu, Hawaii belonging to the ubiquitous and versatile Roseobacter clade of the alphaproteobacterial family Rhodobacteraceae. Here we describe the preliminary characteristics of strain HIMB11, including annotation of the draft genome sequence and comparative genomic analysis with other members of the Roseobacter lineage. The 3,098,747 bp draft genome is arranged in 34 contigs and contains 3,183 protein-coding genes and 54 RNA genes. Phylogenomic and 16S rRNA gene analyses indicate that HIMB11 represents a unique sublineage within the Roseobacter clade. Comparison with other publicly available genome sequences from members of the Roseobacter lineage reveals that strain HIMB11 has the genomic potential to utilize a wide variety of energy sources (e.g. organic matter, reduced inorganic sulfur, light, carbon monoxide), while possessing a reduced number of substrate transporters

Iron depletion in the deep chlorophyll maximum: mesoscale eddies as natural iron fertilization experiments

© The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Hawco, N. J., Barone, B., Church, M. J., Babcock-Adams, L., Repeta, D. J., Wear, E. K., Foreman, R. K., Bjorkman, K. M., Bent, S., Van Mooy, B. A. S., Sheyn, U., DeLong, E. F., Acker, M., Kelly, R. L., Nelson, A., Ranieri, J., Clemente, T. M., Karl, D. M., & John, S. G. Iron depletion in the deep chlorophyll maximum: mesoscale eddies as natural iron fertilization experiments. Global Biogeochemical Cycles, 35(12), (2021): e2021GB007112, https://doi.org/10.1029/2021GB007112.In stratified oligotrophic waters, phytoplankton communities forming the deep chlorophyll maximum (DCM) are isolated from atmospheric iron sources above and remineralized iron sources below. Reduced supply leads to a minimum in dissolved iron (dFe) near 100 m, but it is unclear if iron limits growth at the DCM. Here, we propose that natural iron addition events occur regularly with the passage of mesoscale eddies, which alter the supply of dFe and other nutrients relative to the availability of light, and can be used to test for iron limitation at the DCM. This framework is applied to two eddies sampled in the North Pacific Subtropical Gyre. Observations in an anticyclonic eddy center indicated downwelling of iron-rich surface waters, leading to increased dFe at the DCM but no increase in productivity. In contrast, uplift of isopycnals within a cyclonic eddy center increased supply of both nitrate and dFe to the DCM, and led to dominance of picoeukaryotic phytoplankton. Iron addition experiments did not increase productivity in either eddy, but significant enhancement of leucine incorporation in the light was observed in the cyclonic eddy, a potential indicator of iron stress among Prochlorococcus. Rapid cycling of siderophores and low dFe:nitrate uptake ratios also indicate that a portion of the microbial community was stressed by low iron. However, near-complete nitrate drawdown in this eddy, which represents an extreme case in nutrient supply compared to nearby Hawaii Ocean Time-series observations, suggests that recycling of dFe in oligotrophic ecosystems is sufficient to avoid iron limitation in the DCM under typical conditions.The expedition and analyses were supported by the Simons Foundation SCOPE Grant 329108 to S. G. John, M. J. Church, D. J. Repeta, B. Van Mooy, E. F. DeLong, and D. M. Karl. N. J. Hawco was supported by a Simons Foundation Marine Microbial Ecology and Evolution postdoctoral fellowship (602538) and Simons Foundation grant 823167