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1.  Resuscitation of the rare biosphere contributes to pulses of ecosystem activity 
Dormancy is a life history trait that may have important implications for linking microbial communities to the functioning of natural and managed ecosystems. Rapid changes in environmental cues may resuscitate dormant bacteria and create pulses of ecosystem activity. In this study, we used heavy-water (H182O) stable isotope probing (SIP) to identify fast-growing bacteria that were associated with pulses of trace gasses (CO2, CH4, and N2O) from different ecosystems [agricultural site, grassland, deciduous forest, and coniferous forest (CF)] following a soil-rewetting event. Irrespective of ecosystem type, a large fraction (69–74%) of the bacteria that responded to rewetting were below detection limits in the dry soils. Based on the recovery of sequences, in just a few days, hundreds of rare taxa increased in abundance and in some cases became dominant members of the rewetted communities, especially bacteria belonging to the Sphingomonadaceae, Comamonadaceae, and Oxalobacteraceae. Resuscitation led to dynamic shifts in the rank abundance of taxa that caused previously rare bacteria to comprise nearly 60% of the sequences that were recovered in rewetted communities. This rapid turnover of the bacterial community corresponded with a 5–20-fold increase in the net production of CO2 and up to a 150% reduction in the net production of CH4 from rewetted soils. Results from our study demonstrate that the rare biosphere may account for a large and dynamic fraction of a community that is important for the maintenance of bacterial biodiversity. Moreover, our findings suggest that the resuscitation of rare taxa from seed banks contribute to ecosystem functioning.
doi:10.3389/fmicb.2015.00024
PMCID: PMC4311709
CO2 pulses; dormancy; desiccation; dominance; stable isotope probing (SIP); soil rewetting; seed bank; rarity
2.  Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial Diversity 
mBio  2014;5(4):e01371-14.
ABSTRACT
Microbial communities typically contain many rare taxa that make up the majority of the observed membership, yet the contribution of this microbial “rare biosphere” to community dynamics is unclear. Using 16S rRNA amplicon sequencing of 3,237 samples from 42 time series of microbial communities from nine different ecosystems (air; marine; lake; stream; adult human skin, tongue, and gut; infant gut; and brewery wastewater treatment), we introduce a new method to detect typically rare microbial taxa that occasionally become very abundant (conditionally rare taxa [CRT]) and then quantify their contributions to temporal shifts in community structure. We discovered that CRT made up 1.5 to 28% of the community membership, represented a broad diversity of bacterial and archaeal lineages, and explained large amounts of temporal community dissimilarity (i.e., up to 97% of Bray-Curtis dissimilarity). Most of the CRT were detected at multiple time points, though we also identified “one-hit wonder” CRT that were observed at only one time point. Using a case study from a temperate lake, we gained additional insights into the ecology of CRT by comparing routine community time series to large disturbance events. Our results reveal that many rare taxa contribute a greater amount to microbial community dynamics than is apparent from their low proportional abundances. This observation was true across a wide range of ecosystems, indicating that these rare taxa are essential for understanding community changes over time.
IMPORTANCE
Microbial communities and their processes are the foundations of ecosystems. The ecological roles of rare microorganisms are largely unknown, but it is thought that they contribute to community stability by acting as a reservoir that can rapidly respond to environmental changes. We investigated the occurrence of typically rare taxa that very occasionally become more prominent in their communities (“conditionally rare”). We quantified conditionally rare taxa in time series from a wide variety of ecosystems and discovered that not only were conditionally rare taxa present in all of the examples, but they also contributed disproportionately to temporal changes in diversity when they were most abundant. This result indicates an important and general role for rare microbial taxa within their communities.
doi:10.1128/mBio.01371-14
PMCID: PMC4161262  PMID: 25028427
3.  A Source of Terrestrial Organic Carbon to Investigate the Browning of Aquatic Ecosystems 
PLoS ONE  2013;8(10):e75771.
There is growing evidence that terrestrial ecosystems are exporting more dissolved organic carbon (DOC) to aquatic ecosystems than they did just a few decades ago. This “browning” phenomenon will alter the chemistry, physics, and biology of inland water bodies in complex and difficult-to-predict ways. Experiments provide an opportunity to elucidate how browning will affect the stability and functioning of aquatic ecosystems. However, it is challenging to obtain sources of DOC that can be used for manipulations at ecologically relevant scales. In this study, we evaluated a commercially available source of humic substances (“Super Hume”) as an analog for natural sources of terrestrial DOC. Based on chemical characterizations, comparative surveys, and whole-ecosystem manipulations, we found that the physical and chemical properties of Super Hume are similar to those of natural DOC in aquatic and terrestrial ecosystems. For example, Super Hume attenuated solar radiation in ways that will not only influence the physiology of aquatic taxa but also the metabolism of entire ecosystems. Based on its chemical properties (high lignin content, high quinone content, and low C:N and C:P ratios), Super Hume is a fairly recalcitrant, low-quality resource for aquatic consumers. Nevertheless, we demonstrate that Super Hume can subsidize aquatic food webs through 1) the uptake of dissolved organic constituents by microorganisms, and 2) the consumption of particulate fractions by larger organisms (i.e., Daphnia). After discussing some of the caveats of Super Hume, we conclude that commercial sources of humic substances can be used to help address pressing ecological questions concerning the increased export of terrestrial DOC to aquatic ecosystems.
doi:10.1371/journal.pone.0075771
PMCID: PMC3790824  PMID: 24124511
4.  Pharmacokinetic Evaluation of Intranasally Administered Vinyl Polymer-Coated Lorazepam Microparticles in Rabbits 
The AAPS Journal  2012;14(2):218-224.
The intranasal (IN) administration of lorazepam is desirable in order to maximize speed of onset and minimise carry-over sedation; however, this benzodiazepine is prone to chemical hydrolysis and poor airway retention, and thus, innovative epithelial presentation is required. The aim of this study was to understand how the in situ self-assembly of a mucoretentive delivery system, formed by the dissolution of vinyl polymer-coated microparticles in the nasal mucosa, would influence lorazepam pharmacokinetics (PK). IN administration of the uncoated lorazepam powder (particle size, 6.7 ± 0.1 μm) generated a biphasic PK profile, which was indicative of sequential intranasal and oral absorption (n = 6; dose, 5 mg/kg). Coating the drug with the vinyl polymer, MP1 (9.9 ± 0.5 μm with 38.8 ± 14.0%, w/w lorazepam) and MP2 (10.7 ± 0.1 μm with 47.0 ± 1.0%, w/w lorazepam), allowed rapid systemic absorption (MP1, Tmax 14.2 ± 4.9 min; MP2, Tmax 9.3 ± 3.8 min) in rabbits and modified the PK profiles in a manner that suggested successful nasal retention. The poly(vinyl pyrrolidone)-rich MP2 system provided the best comparative bioavailability, it prolonged the early-phase nasal drug absorption and minimised drug mucociliary clearance, which correlated well with the intermolecular hydrogen-bond-driven vinyl polymer interactions observed in vitro.
doi:10.1208/s12248-012-9325-x
PMCID: PMC3326174  PMID: 22396304
intranasal; lorazepam; microparticles; pharmacokinetics; poly(vinyl alcohol)
5.  Spatial and temporal scales of aquatic bacterial beta diversity 
Understanding characteristic variation in aquatic bacterial community composition (BCC) across space and time can inform us about processes driving community assembly and the ability of bacterial communities to respond to perturbations. In this study, we synthesize BCC data from north temperate lakes to evaluate our current understanding of how BCC varies across multiple scales in time and space. A hierarchy of average similarity emerged with the highest similarity found among samples collected within the same lake, especially within the same basin, followed by similarity among samples collected through time within the same lake, and finally similarity among samples collected from different lakes. Using decay of similarity across time and space, we identified equivalent temporal (1 day) and spatial (10 m) scales of BCC variation. Finally, we identify an intriguing pattern of contrasting patterns of intra- and inter-annual BCC variation in two lakes. We argue our synthesis of spatio-temporal variation of aquatic BCC informs expectations for the response of aquatic bacterial communities to perturbation and environmental change. However, further long-term temporal observations will be needed to develop a general understanding of inter-annual BCC variation and our ability to use aquatic BCC as a sensitive metric of environmental change.
doi:10.3389/fmicb.2012.00318
PMCID: PMC3431545  PMID: 22969757
lake; beta diversity; spatial; temporal
6.  A Guide to the Natural History of Freshwater Lake Bacteria†  
Summary: Freshwater bacteria are at the hub of biogeochemical cycles and control water quality in lakes. Despite this, little is known about the identity and ecology of functionally significant lake bacteria. Molecular studies have identified many abundant lake bacteria, but there is a large variation in the taxonomic or phylogenetic breadths among the methods used for this exploration. Because of this, an inconsistent and overlapping naming structure has developed for freshwater bacteria, creating a significant obstacle to identifying coherent ecological traits among these groups. A discourse that unites the field is sorely needed. Here we present a new freshwater lake phylogeny constructed from all published 16S rRNA gene sequences from lake epilimnia and propose a unifying vocabulary to discuss freshwater taxa. With this new vocabulary in place, we review the current information on the ecology, ecophysiology, and distribution of lake bacteria and highlight newly identified phylotypes. In the second part of our review, we conduct meta-analyses on the compiled data, identifying distribution patterns for bacterial phylotypes among biomes and across environmental gradients in lakes. We conclude by emphasizing the role that this review can play in providing a coherent framework for future studies.
doi:10.1128/MMBR.00028-10
PMCID: PMC3063352  PMID: 21372319
7.  Randomized study evaluating testosterone recovery using short-versus long-acting luteinizing hormone releasing hormone agonists 
Introduction:
We sought to compare the rate of return of testosterone levels and sexual function in men with prostate cancer receiving longer acting, 3-month preparation of luteinizing hormone-releasing hormone agonist (L-LHRH-A) versus shorter acting, 1-month preparation of luteinizing hormone-releasing hormone agonist (S-LHRH-A).
Methods and Materials:
Men with low to intermediate risk localized prostate cancer were randomized to either L-LHRH-A (2–3 month duration LHRH-A) or S-LHRH-A (6-1 month duration LHRH-A) of androgen suppression therapy (AST) and prostate brachytherapy using iodine-125 radioisotopes. Serum total testosterone levels and PSA were recorded every 2 months for 2 years.
Results:
A planned target sample size of 100 was not achieved due to insufficient accrual. A total of 55 patients were randomized and 46 were used for analysis. The median time to recovery of testosterone to baseline levels (calculated from end of AST) was 8 and 4 months in the L-LHRH-A and S-LHRH-A arms, respectively (p = 0.268). The median time to testosterone recovery to lower limit of reference range was 4 and 2 months respectively (p = 0.087).
Interpretation:
This randomized study, which failed to reach accrual target, showed a trend towards more rapid recovery of testosterone levels using shorter acting LHRH-A. Another randomized study would be required to validate these findings. Currently, there is insufficient evidence to recommend the use of shorter acting LHRH-A as a means of providing more rapid recovery of testosterone levels.
doi:10.5489/cuaj.10102
PMCID: PMC3114026  PMID: 21672478
8.  Systemic inflammation and decline in lung function in a general population: a prospective study 
Thorax  2007;62(6):515-520.
Background
An increase in levels of C‐reactive protein (CRP), a marker of systemic inflammation, is associated with reduced forced expiratory volume in 1 s (FEV1), supporting the hypothesis that the pathophysiology of chronic obstructive pulmonary disease has a systemic inflammatory component. However, few large studies have assessed the relationship between systemic inflammation as measured by CRP and decline in lung function prospectively in a randomly selected population.
Methods
In 1991, data were collected on FEV1 and forced vital capacity (FVC) and a blood sample was taken from 2442 randomly selected adults in a community‐based cohort. In 2000 these measures were repeated in 1301 individuals. The level of serum CRP was analysed in these samples from 1991 and 2000.
Results
In cross‐sectional analyses of data from 1991 and 2000, serum CRP levels were inversely related to FEV1 and FVC. After adjustment for smoking and other confounders, the difference in FEV1 was reduced by −9 ml (95% CI –13 to –5) and –7 ml (95% CI –13 to –2) for each mg/l increment in serum CRP in 1991 and 2000, respectively. There was no significant association between baseline serum CRP levels and decline in FEV1 and FVC over 9 years.
Conclusions
Although serum CRP levels are inversely associated with lung function in cross‐sectional studies, there was no effect of a marker of systemic inflammation on decline in lung function over 9 years.
doi:10.1136/thx.2006.066969
PMCID: PMC2117221  PMID: 17251312
9.  Phylogenetic Ecology of the Freshwater Actinobacteria acI Lineage▿ †  
Applied and Environmental Microbiology  2007;73(22):7169-7176.
The acI lineage of freshwater Actinobacteria is a cosmopolitan and often numerically dominant member of lake bacterial communities. We conducted a survey of acI 16S rRNA genes and 16S-23S rRNA internal transcribed spacer regions from 18 Wisconsin lakes and used standard nonphylogenetic and phylogenetic statistical approaches to investigate the factors that determine acI community composition at the local scale (within lakes) and at the regional scale (across lakes). Phylogenetic reconstruction of 434 acI 16S rRNA genes revealed a well-defined and highly resolved phylogeny. Eleven previously unrecognized monophyletic clades, each with ≥97.9% within-clade 16S rRNA gene sequence identity, were identified. Clade community similarity positively correlated with lake environmental similarity but not with geographic distance, implying that the lakes represent a single biotic region containing environmental filters for communities that have similar compositions. Phylogenetically disparate clades within the acI lineage were most abundant at the regional scale, and local communities were comprised of more closely related clades. Lake pH was a strong predictor of the community composition, but only when lakes with a pH below 6 were included in the data set. In the remaining lakes (pH above 6) biogeographic patterns in the landscape were instead a predictor of the observed acI community structure. The nonrandom distribution of the newly defined acI clades suggests potential ecophysiological differences between the clades, with acI clades AI, BII, and BIII preferring acidic lakes and acI clades AII, AVI, and BI preferring more alkaline lakes.
doi:10.1128/AEM.00794-07
PMCID: PMC2168227  PMID: 17827330
10.  Comparison of Primer Sets for Use in Automated Ribosomal Intergenic Spacer Analysis of Aquatic Bacterial Communities: an Ecological Perspective▿  
Two primer sets for automated ribosomal intergenic spacer analysis (ARISA) were used to assess the bacterial community composition (BCC) in Lake Mendota, Wisconsin, over 3 years. Correspondence analysis revealed differences in community profiles generated by different primer sets, but overall ecological patterns were conserved in each case. ARISA is a powerful tool for evaluating BCC change through space and time, regardless of the specific primer set used.
doi:10.1128/AEM.02130-06
PMCID: PMC1796982  PMID: 17122397

Results 1-10 (10)