Core Microbial Functional Activities in Ocean Environments Revealed by Global Metagenomic Profiling Analyses

Metagenomics-based functional profiling analysis is an effective means of gaining deeper insight into the composition of marine microbial populations and developing a better understanding of the interplay between the functional genome content of microbial communities and abiotic factors. Here we present a comprehensive analysis of 24 datasets covering surface and depth-related environments at 11 sites around the world's oceans. The complete datasets comprises approximately 12 million sequences, totaling 5,358 Mb. Based on profiling patterns of Clusters of Orthologous Groups (COGs) of proteins, a core set of reference photic and aphotic depth-related COGs, and a collection of COGs that are associated with extreme oxygen limitation were defined. Their inferred functions were utilized as indicators to characterize the distribution of light- and oxygen-related biological activities in marine environments. The results reveal that, while light level in the water column is a major determinant of phenotypic adaptation in marine microorganisms, oxygen concentration in the aphotic zone has a significant impact only in extremely hypoxic waters. Phylogenetic profiling of the reference photic/aphotic gene sets revealed a greater variety of source organisms in the aphotic zone, although the majority of individual photic and aphotic depth-related COGs are assigned to the same taxa across the different sites. This increase in phylogenetic and functional diversity of the core aphotic related COGs most probably reflects selection for the utilization of a broad range of alternate energy sources in the absence of light.This work was supported by King Abdullah University for Science and Technology Global Collaborative Partners (GCR) program. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Aerobic methanotrophic communities at the Red Sea brine-seawater interface

The central rift of the Red Sea contains 25 brine pools with different physicochemical conditions, dictating the diversity and abundance of the microbial community. Three of these pools, the Atlantis II, Kebrit and Discovery Deeps, are uniquely characterized by a high concentration of hydrocarbons. The brine-seawater interface, described as an anoxic-oxic (brine-seawater) boundary, is characterized by a high methane concentration, thus favoring aerobic methane oxidation. The current study analyzed the aerobic free–living methane-oxidizing bacterial communities that potentially contribute to methane oxidation at the brine-seawater interfaces of the three aforementioned brine pools, using metagenomic pyrosequencing, 16S rRNA pyrotags and pmoA library constructs. The sequencing of 16S rRNA pyrotags revealed that these interfaces are characterized by high microbial community diversity. Signatures of aerobic methane-oxidizing bacteria were detected in the Atlantis II Interface (ATII-I) and the Kebrit Deep Upper (KB-U) and Lower (KB-L) brine-seawater interfaces. Through phylogenetic analysis of pmoA, we further demonstrated that the ATII-I aerobic methanotroph community is highly diverse. We propose four ATII-I pmoA clusters. Most importantly, cluster 2 groups with marine methane seep methanotrophs, and cluster 4 represent a unique lineage of an uncultured bacterium with divergent alkane monooxygenases. Moreover, non-metric multidimensional scaling (NMDS) based on the ordination of putative enzymes involved in methane metabolism showed that the Kebrit interface layers were distinct from the ATII-I and DD-I brine-seawater interfaces

Clustering of the 176 depth-related COGs.

<p>(<b>A</b>) Hierarchical clustering of the 176 depth-related COGs in the 24 datasets. Clustering analysis is based on the normalized abundance profile of the 176 depth-related COGs that were shared by the three reference water columns (ATII, ALOHA and BATS) and significantly differed in abundance within at least one of them (details in Materials and Methods). The height indicates the relative distance between datasets. Bootstrap confidence values above 60 for the nodes are shown. The heatmap is shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0097338#pone.0097338.s003" target="_blank">fig. S3A</a>. (<b>B</b>) Location of the boundary between the photic and aphotic zones in each of the four water columns. The arrows indicate the depth at which PAR reaches 1% of the level at the surface. (<b>C</b>) Hierarchical clustering of the photic/aphotic global-core depth-related COGs. 82 COGs that showed statistically significant difference (Welch's test, FDR-corrected, p≤1E-04) in their normalized abundance between the photic and the aphotic groups of datasets were selected to establish a photic/aphotic global-core, depth-related reference set. 54 COGs had significantly higher abundance in the photic datasets (Group I, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0097338#pone.0097338.s004" target="_blank">table S4A in file S1</a>); contrary to the remaining 28 aphotic related COGs (Group II, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0097338#pone.0097338.s004" target="_blank">table S4B in file S1</a>). Bootstrap confidence values for the major nodes are shown. Heatmap coloring reflects the Z score of normalized abundances of each COG across all clustered datasets (details in Materials and Methods).</p

Taxonomical assignments of photic and aphotic depth-related COGs at the phylum level for the selected datasets.

<p>Reads assigned to COGs were compared to the NCBI nr database using BLASTX (E-value cutoff 1e-05) and the taxonomical identifiers of the best matches were retrieved. Subsequently, tables of relative frequency of taxa per COG per dataset were generated (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0097338#pone.0097338.s004" target="_blank">tables S6A and S6B in file S1</a>) and presented as heatmaps. The 10 phyla that have the highest average numbers of photic (<b>A</b>) and aphotic (<b>B</b>) COGs per site are presented. The taxa are sorted by the decreasing of their abundance. Datasets of the shallowest samples of the ALOHA, ATII and BATS water columns and single-depth datasets from GOS018, GOS023, GOS034, GOS114 and Mediterranean sites were used for the analysis of the photic related COGs, whereas the deepest datasets from the ALOHA, ATII and BATS water columns, and single-depth datasets from Marmara, PRT and ALOHA (4,000 m), were employed in the case of the aphotic related COGs. This analysis was based on a total of 36,938 sequences (24919 sequences are photic, and 12019 are aphotic).</p

Abundance ratios of photic to aphotic related COGs.

<p>(<b>A</b>) Mean abundance ratios of photic to aphotic related COGs for datasets from the reference water columns, the Iquique water column, and from single-depth datasets. This analysis was initially determined using the 82-COG global-core, depth-related reference set, as described in Materials and Methods. Applying the ratios for the photic and aphotic datasets from the reference water columns, ratio ranges (mean±two SD) were established to indicate photic or aphotic functional genomic content enrichment. Mean abundance ratios for the Iquique water column and the single-depth datasets were calculated to verify their balance between photic and aphotic related biological functions. The arrows at the top of the diagram indicate the approximate depth of the boundary between photic and aphotic zones in each water column (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0097338#pone-0097338-g001" target="_blank">fig. 1B</a>). (<b>B</b>) Normalized abundance of the deoxyribodipyrimidine photolyase gene (COG0415; <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0097338#pone.0097338.s004" target="_blank">table S4A in file S1</a>) in the 24 datasets obtained from the indicated depths. The average normalized abundance was calculated for the photic and for the aphotic groups of datasets. The bars represent two SD of the mean.</p

Effect of oxygen concentration on the functional genomic content of microbial communities represented in the 24 datasets.

<p>(A) Hierarchical clustering of COGs that significantly influenced by extreme oxygen limitation. Datasets analysis are based on the abundance profile of 18 COGs which significantly differed in abundance levels between an extremely hypoxic environment (Iquique 85-, 110 and 200 m deep, permanent OMZ) and environments with higher D.O. (Fisher's exact test, FDR-corrected, p≤0.05). Bootstrap confidence values for the nodes are shown. Heatmap coloring reflects the Z score of normalized abundances of each COG across all clustered datasets. Roman numbers on the left side of the figure present different groups of COGs as determined by abundance profile across the clustered datasets. (B) Mean abundances of the COGs in group I (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0097338#pone-0097338-g003" target="_blank">figure 3A</a>) as a function of the oxygen concentration. Inset shows the gradual increase in the abundance of these genes in datasets from Marmara 1000 m, Iquique 85 m, Iquique 110 m, and Iquique 200 m, as oxygen concentration drops from 30 µmol.kg⁻¹ to 3.2 µmol.kg⁻¹.</p

Global economic burden of unmet surgical need for appendicitis

Background There is a substantial gap in provision of adequate surgical care in many low- and middle-income countries. This study aimed to identify the economic burden of unmet surgical need for the common condition of appendicitis. Methods Data on the incidence of appendicitis from 170 countries and two different approaches were used to estimate numbers of patients who do not receive surgery: as a fixed proportion of the total unmet surgical need per country (approach 1); and based on country income status (approach 2). Indirect costs with current levels of access and local quality, and those if quality were at the standards of high-income countries, were estimated. A human capital approach was applied, focusing on the economic burden resulting from premature death and absenteeism. Results Excess mortality was 4185 per 100 000 cases of appendicitis using approach 1 and 3448 per 100 000 using approach 2. The economic burden of continuing current levels of access and local quality was US $92 492 million using approach 1 and$73 141 million using approach 2. The economic burden of not providing surgical care to the standards of high-income countries was $95 004 million using approach 1 and$75 666 million using approach 2. The largest share of these costs resulted from premature death (97.7 per cent) and lack of access (97.0 per cent) in contrast to lack of quality. Conclusion For a comparatively non-complex emergency condition such as appendicitis, increasing access to care should be prioritized. Although improving quality of care should not be neglected, increasing provision of care at current standards could reduce societal costs substantially

Global economic burden of unmet surgical need for appendicitis

Background There is a substantial gap in provision of adequate surgical care in many low- and middle-income countries. This study aimed to identify the economic burden of unmet surgical need for the common condition of appendicitis. Methods Data on the incidence of appendicitis from 170 countries and two different approaches were used to estimate numbers of patients who do not receive surgery: as a fixed proportion of the total unmet surgical need per country (approach 1); and based on country income status (approach 2). Indirect costs with current levels of access and local quality, and those if quality were at the standards of high-income countries, were estimated. A human capital approach was applied, focusing on the economic burden resulting from premature death and absenteeism. Results Excess mortality was 4185 per 100 000 cases of appendicitis using approach 1 and 3448 per 100 000 using approach 2. The economic burden of continuing current levels of access and local quality was US $92 492 million using approach 1 and$73 141 million using approach 2. The economic burden of not providing surgical care to the standards of high-income countries was $95 004 million using approach 1 and$75 666 million using approach 2. The largest share of these costs resulted from premature death (97.7 per cent) and lack of access (97.0 per cent) in contrast to lack of quality. Conclusion For a comparatively non-complex emergency condition such as appendicitis, increasing access to care should be prioritized. Although improving quality of care should not be neglected, increasing provision of care at current standards could reduce societal costs substantially

Global fertility in 204 countries and territories, 1950–2021, with forecasts to 2100: a comprehensive demographic analysis for the Global Burden of Disease Study 2021

BackgroundAccurate assessments of current and future fertility—including overall trends and changing population age structures across countries and regions—are essential to help plan for the profound social, economic, environmental, and geopolitical challenges that these changes will bring. Estimates and projections of fertility are necessary to inform policies involving resource and health-care needs, labour supply, education, gender equality, and family planning and support. The Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2021 produced up-to-date and comprehensive demographic assessments of key fertility indicators at global, regional, and national levels from 1950 to 2021 and forecast fertility metrics to 2100 based on a reference scenario and key policy-dependent alternative scenarios. MethodsTo estimate fertility indicators from 1950 to 2021, mixed-effects regression models and spatiotemporal Gaussian process regression were used to synthesise data from 8709 country-years of vital and sample registrations, 1455 surveys and censuses, and 150 other sources, and to generate age-specific fertility rates (ASFRs) for 5-year age groups from age 10 years to 54 years. ASFRs were summed across age groups to produce estimates of total fertility rate (TFR). Livebirths were calculated by multiplying ASFR and age-specific female population, then summing across ages 10–54 years. To forecast future fertility up to 2100, our Institute for Health Metrics and Evaluation (IHME) forecasting model was based on projections of completed cohort fertility at age 50 years (CCF50; the average number of children born over time to females from a specified birth cohort), which yields more stable and accurate measures of fertility than directly modelling TFR. CCF50 was modelled using an ensemble approach in which three sub-models (with two, three, and four covariates variously consisting of female educational attainment, contraceptive met need, population density in habitable areas, and under-5 mortality) were given equal weights, and analyses were conducted utilising the MR-BRT (meta-regression—Bayesian, regularised, trimmed) tool. To capture time-series trends in CCF50 not explained by these covariates, we used a first-order autoregressive model on the residual term. CCF50 as a proportion of each 5-year ASFR was predicted using a linear mixed-effects model with fixed-effects covariates (female educational attainment and contraceptive met need) and random intercepts for geographical regions. Projected TFRs were then computed for each calendar year as the sum of single-year ASFRs across age groups. The reference forecast is our estimate of the most likely fertility future given the model, past fertility, forecasts of covariates, and historical relationships between covariates and fertility. We additionally produced forecasts for multiple alternative scenarios in each location: the UN Sustainable Development Goal (SDG) for education is achieved by 2030; the contraceptive met need SDG is achieved by 2030; pro-natal policies are enacted to create supportive environments for those who give birth; and the previous three scenarios combined. Uncertainty from past data inputs and model estimation was propagated throughout analyses by taking 1000 draws for past and present fertility estimates and 500 draws for future forecasts from the estimated distribution for each metric, with 95% uncertainty intervals (UIs) given as the 2·5 and 97·5 percentiles of the draws. To evaluate the forecasting performance of our model and others, we computed skill values—a metric assessing gain in forecasting accuracy—by comparing predicted versus observed ASFRs from the past 15 years (2007–21). A positive skill metric indicates that the model being evaluated performs better than the baseline model (here, a simplified model holding 2007 values constant in the future), and a negative metric indicates that the evaluated model performs worse than baseline. FindingsDuring the period from 1950 to 2021, global TFR more than halved, from 4·84 (95% UI 4·63–5·06) to 2·23 (2·09–2·38). Global annual livebirths peaked in 2016 at 142 million (95% UI 137–147), declining to 129 million (121–138) in 2021. Fertility rates declined in all countries and territories since 1950, with TFR remaining above 2·1—canonically considered replacement-level fertility—in 94 (46·1%) countries and territories in 2021. This included 44 of 46 countries in sub-Saharan Africa, which was the super-region with the largest share of livebirths in 2021 (29·2% [28·7–29·6]). 47 countries and territories in which lowest estimated fertility between 1950 and 2021 was below replacement experienced one or more subsequent years with higher fertility; only three of these locations rebounded above replacement levels. Future fertility rates were projected to continue to decline worldwide, reaching a global TFR of 1·83 (1·59–2·08) in 2050 and 1·59 (1·25–1·96) in 2100 under the reference scenario. The number of countries and territories with fertility rates remaining above replacement was forecast to be 49 (24·0%) in 2050 and only six (2·9%) in 2100, with three of these six countries included in the 2021 World Bank-defined low-income group, all located in the GBD super-region of sub-Saharan Africa. The proportion of livebirths occurring in sub-Saharan Africa was forecast to increase to more than half of the world's livebirths in 2100, to 41·3% (39·6–43·1) in 2050 and 54·3% (47·1–59·5) in 2100. The share of livebirths was projected to decline between 2021 and 2100 in most of the six other super-regions—decreasing, for example, in south Asia from 24·8% (23·7–25·8) in 2021 to 16·7% (14·3–19·1) in 2050 and 7·1% (4·4–10·1) in 2100—but was forecast to increase modestly in the north Africa and Middle East and high-income super-regions. Forecast estimates for the alternative combined scenario suggest that meeting SDG targets for education and contraceptive met need, as well as implementing pro-natal policies, would result in global TFRs of 1·65 (1·40–1·92) in 2050 and 1·62 (1·35–1·95) in 2100. The forecasting skill metric values for the IHME model were positive across all age groups, indicating that the model is better than the constant prediction. InterpretationFertility is declining globally, with rates in more than half of all countries and territories in 2021 below replacement level. Trends since 2000 show considerable heterogeneity in the steepness of declines, and only a small number of countries experienced even a slight fertility rebound after their lowest observed rate, with none reaching replacement level. Additionally, the distribution of livebirths across the globe is shifting, with a greater proportion occurring in the lowest-income countries. Future fertility rates will continue to decline worldwide and will remain low even under successful implementation of pro-natal policies. These changes will have far-reaching economic and societal consequences due to ageing populations and declining workforces in higher-income countries, combined with an increasing share of livebirths among the already poorest regions of the world. FundingBill & Melinda Gates Foundation