scholarly journals Microbe biogeography tracks water masses in a dynamic oceanic frontal system

2017 ◽  
Vol 4 (3) ◽  
pp. 170033 ◽  
Author(s):  
Anni Djurhuus ◽  
Philipp H. Boersch-Supan ◽  
Svein-Ole Mikalsen ◽  
Alex D. Rogers
Keyword(s):  
Microbial Communities ◽  
Regional Scale ◽  
Water Masses ◽  
Latitudinal Gradients ◽  
Intermediate Water ◽  
Depth Stratum ◽  
Regional Patterns ◽  
Southwest Indian Ocean ◽  
Microbial Biogeography ◽  
Environmental Selection

Dispersal limitation, not just environmental selection, plays an important role in microbial biogeography. The distance–decay relationship is thought to be weak in habitats where dispersal is high, such as in the pelagic environment, where ocean currents facilitate microbial dispersal. Most studies of microbial community composition to date have observed little geographical heterogeneity on a regional scale (100 km). We present a study of microbial communities across a dynamic frontal zone in the southwest Indian Ocean and investigate the spatial structure of the microbes with respect to the different water masses separated by these fronts. We collected 153 samples of free-living microorganisms from five seamounts located along a gradient from subtropical to subantarctic waters and across three depth layers: (i) the sub-surface chlorophyll maximum (approx. 40 m), (ii) the bottom of the euphotic zone (approx. 200 m), and (iii) the benthic boundary layer (300–2000 m). Diversity and abundance of microbial operational taxonomic units (OTUs) were assessed by amplification and sequencing of the 16S rRNA gene on an Illumina MiSeq platform. Multivariate analyses showed that microbial communities were structured more strongly by depth than by latitude, with similar phyla occurring within each depth stratum across seamounts. The deep layer was homogeneous across the entire survey area, corresponding to the spread of Antarctic intermediate water. However, within both the sub-surface layer and the intermediate depth stratum there was evidence for OTU turnover across fronts. The microbiome of these layers appears to be divided into three distinct biological regimes corresponding to the subantarctic surface water, the convergence zone and subtropical. We show that microbial biogeography across depth and latitudinal gradients is linked to the water masses the microbes persist in, resulting in regional patterns of microbial biogeography that correspond to the regional scale physical oceanography.

scholarly journals Recent hydrological status of the Aegean Sea derived from free drifting profilers

2021 ◽  
Author(s):  
DIMITRIS KASSIS ◽  
GERASIMOS KORRES
Keyword(s):  
Physical Properties ◽  
Mediterranean Sea ◽  
Water Column ◽  
Eastern Mediterranean ◽  
Temporal Distribution ◽  
Aegean Sea ◽  
Water Masses ◽  
Latitudinal Gradients ◽  
Intermediate Water ◽  
Argo Floats

Being a semi-enclosed basin of the Mediterranean Sea, the Aegean Sea comprises a complex hydrology that plays a significant role in the hydrology of the Eastern Mediterranean Sea. Its interaction with many sub-basins, along with its contribution towards the formation of deep and intermediate water, makes it an ideal case for the study of hydrological changes in transitional areas. Since 2010, the operational monitoring of the basin has been significantly enriched due to the deployment of autonomous free-drifting profilers (Argo floats) under the framework of the newly formed Greek Argo Research Infrastructure activities. In this study the hydrological status of the area is examined for the period 2010 - 2017 using the temperature and salinity profiles acquired from Argo floats that operated in the basin. The profiles are analyzed together with complementary remote sensing and model outputs datasets in order to present the spatio-temporal distribution of the co-existent water masses and shed light on hydrological features and changes that took place throughout the basin in an attempt to reassess its hydrological status during the last decade. The distribution of the physical properties in different sub-regions and their interaction is examined reconstructing a general picture of strong latitudinal gradients in the T-S and σθ fields from the upper layers towards the deeper zones. Interannually, findings indicate changes of the Aegean water masses structure within the water-column. Deep homogenization in the upper layers is recorded mainly during the winter periods of 2011-2012, 2014-2015 and 2016-2017 in the southern, central, and northern parts of the area accordingly. The observed dense water formation events, along with mixing and advection appear to alterate the water column physical properties structure and affect the dynamics of the surface and sub-surface dominant water masses in the Aegean. The results further highlight the valuable information that can be extracted from the operation of free-drifting profilers in enclosed marginal seas similar to the Aegean case.

scholarly journals A phylogenetic transform enhances analysis of compositional microbiota data

2016 ◽  
Author(s):  
Justin D Silverman ◽  
Alex Washburne ◽  
Sayan Mukherjee ◽  
Lawrence A David
Keyword(s):  
Microbial Communities ◽  
Relative Abundance ◽  
Dominant Role ◽  
Phylogenetic Information ◽  
Abundance Data ◽  
Sequencing Technologies ◽  
Environmental Selection ◽  
Health And Disease ◽  
High Throughput Dna Sequencing ◽  
Spurious Results

ABSTRACTHigh-throughput DNA sequencing technologies have revolutionized the study of microbial communities (microbiota) and have revealed their importance in both human health and disease. However, due to technical limitations, data from microbiota surveys reflect the relative abundance of bacterial taxa and not their absolute levels. It is well known that applying common statistical methods, such as correlation or hypothesis testing, to relative abundance data can lead to spurious results. Here, we introduce the PhILR transform, a data transform that utilizes microbial phylogenetic information. This transform enables off-the-shelf statistical tools to be applied to microbiota surveys free from artifacts usually associated with analysis of relative abundance data. Using environmental and human-associated microbial community datasets as benchmarks, we find that the PhILR transform significantly improves the performance of distance-based and machine learning-based statistics, boosting the accuracy of widely used algorithms on reference benchmarks by 90%. Because the PhILR transform relies on bacterial phylogenies, statistics applied in the PhILR coordinate system are also framed within an evolutionary perspective. Regression on PhILR transformed human microbiota data identified evolutionarily neighboring bacterial clades that may have differentiated to adapt to distinct body sites. Variance statistics showed that the degree of covariation of bacterial clades across human body sites tended to increase with phylogenetic relatedness between clades. These findings support the hypothesis that environmental selection, not competition between bacteria, plays a dominant role in structuring human-associated microbial communities.

scholarly journals Climatic niche predicts the landscape structure of locally adaptive standing genetic variation

2019 ◽  
Author(s):  
Vikram E. Chhatre ◽  
Karl C. Fetter ◽  
Andrew V. Gougherty ◽  
Matthew C. Fitzpatrick ◽  
Raju Y. Soolanayakanahally ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Stress Responses ◽  
Latitudinal Gradients ◽  
Intraspecific Diversity ◽  
Climatic Niche ◽  
Selection Pressures ◽  
Balsam Poplar ◽  
Environmental Selection ◽  
Locally Adaptive ◽  
Spatially Varying

AbstractWithin a species’ range, intraspecific diversity in the form of adaptive standing genetic variation (SGV) may be non-randomly clustered into different geographic regions, reflecting the combined effects of historical range movements and spatially-varying natural selection. As a consequence of a patchy distribution of adaptive SGV, populations in different parts of the range are likely to vary in their capacity to respond to changing selection pressures, especially long-lived sessile organisms like forest trees. However, the spatial distribution of adaptive SGV across the landscape is rarely considered when predicting species responses to environmental change. Here, we use a landscape genomics approach to estimate the distribution of adaptive SGV along spatial gradients reflecting the expansion history and contemporary climatic niche of balsam poplar, Populus balsamifera (Salicaceae), a widely distributed forest tree with a transcontinental distribution in North America. By scanning the genome for signatures of spatially varying local adaptation, we estimated how adaptive SGV has been shaped by geographic distance from the rear range edge (expansion history) versus proximity to the current center of the climatic niche (environmental selection). We found that adaptive SGV was strongly structured by the current climatic niche, with surprisingly little importance attributable to historical effects such as migration out of southern refugia. As expected, the effect of the climatic niche on SGV was strong for genes whose expression is responsive to abiotic stress (drought), although genes upregulated under biotic (wounding) stress also contained SGV that followed climatic and latitudinal gradients. The latter result could reflect parallel selection pressures, or co-regulation of functional pathways involved in both abiotic and biotic stress responses. Our study in balsam poplar suggests that clustering of locally adaptive SGV within ranges primarily reflects spatial proximity within the contemporary climatic niche – an important consideration for the design of effective strategies for biodiversity conservation and avoidance of maladaptation under climate change.

scholarly journals Neutral processes and high inter-annual turnover shape the assembly of soil bacterial communities in a Mediterranean watershed

2019 ◽  
Author(s):  
Myrto Tsiknia ◽  
Stilianos Fodelianakis ◽  
Nikolaos P. Nikolaidis ◽  
Nikolaos V. Paranychianakis
Keyword(s):  
Stochastic Processes ◽  
Microbial Communities ◽  
Bacterial Communities ◽  
Ecosystem Functioning ◽  
Soil Microbial Communities ◽  
Soil Bacterial Communities ◽  
Environmental Selection ◽  
Mediterranean Landscapes ◽  
Soil Bacterial ◽  
Annual Turnover

AbstractThere is a renewed interest in recent years on the ecological processes (stochastic vs selective) driving the assembly of microbial communities. Such information could potentially improve our understanding on ecosystem functioning and resilience to disturbances, ecosystem response to environmental shifts, and adoption of sustainable soil management practices. Herein, employing a suite of existing methodologies, we show that stochastic processes have an important role on the assembly of soil bacterial communities at a Mediterranean watershed. Moreover, we document that the relative contribution of assembly processes varies over the years. The observed intensification of stochastic processes was accompanied by a decrease in the contribution of variable selection in favor of homogeneous selection and dispersal and this trend was only marginally affected by land use (natural vs agricultural lands) or soil depth. Our study also revealed a high inter-annual turnover of soil microbial communities that was likely stimulated by the weak environmental selection and the prevailing environmental conditions (drying-wetting cycles) in Mediterranean landscapes, implying potential impacts on ecosystem functioning and our ability to predict soil response to environmental shifts. Using nitrogen mineralization rate (NMR) as a representative function we document highly variable NMR over the sampling years, land uses and soil depths and lack of significant associations with the monitored environmental variables and individual taxa. In summary, our study provides novel insights on the organization and functioning of microbial communities at Mediterranean ecosystems and sets directions towards a more advanced understanding of the relationships among environmental factors, microbial community structure, and ecosystem functioning that could contribute to sustainable management of these severely degraded ecosystems.

scholarly journals Characterization of the Atlantic Water and Levantine Intermediate Water in the Mediterranean Sea using Argo Float Data

2021 ◽  
Author(s):  
Giusy Fedele ◽  
Elena Mauri ◽  
Giulio Notarstefano ◽  
Pierre Marie Poulain
Keyword(s):  
Mediterranean Sea ◽  
Thermohaline Circulation ◽  
Internal Variability ◽  
Warming Trend ◽  
Atlantic Water ◽  
Western Mediterranean ◽  
Water Masses ◽  
Intermediate Water ◽  
Starting Point ◽  
The Mediterranean

Abstract. The Atlantic Water (AW) and Levantine Intermediate Water (LIW) are important water masses that play a crucial role in the internal variability of the Mediterranean thermohaline circulation. In particular, their variability and interaction, along with other water masses that characterize the Mediterranean basin, such as the Western Mediterranean Deep Water (WMDW), contribute to modify the Mediterranean Outflow through the Gibraltar Strait and hence may influence the stability of the global thermohaline circulation. This work aims to characterize the AW and LIW in the Mediterranean Sea, taking advantage of the large observational dataset provided by Argo floats from 2001 to 2019. Using different diagnostics, the AW and LIW were identified, highlighting the inter-basin variability and the strong zonal gradient that characterize the two water masses in this marginal sea. Their temporal variability was also investigated focusing on trends and spectral features which constitute an important starting point to understand the mechanisms that are behind their variability. A clear salinification and warming trend have characterized the AW and LIW in the last two decades (~0.007 and 0.008 yr−1; 0.018 and 0.007 °C yr−1, respectively). The salinity and temperature trends found at subbasin scale are in good agreement with previous results. The strongest trends are found in the Adriatic basin in both the AW and LIW properties. A subbasin dependent spectral variability emerges in the AW and LIW salinity timeseries with peaks between 2 and 10 years.

scholarly journals Parallel decadal variability of inferred water temperatures for Northern and Southern Hemisphere intermediate water masses

2014 ◽  
Vol 41 (4) ◽  
pp. 1232-1237 ◽  
Author(s):  
Ronald Thresher ◽  
John Morrongiello ◽  
Bernadette M. Sloyan ◽  
Kyne Krusic-Golub ◽  
Samuel Shephard ◽  
...  
Keyword(s):  
Southern Hemisphere ◽  
Decadal Variability ◽  
Water Masses ◽  
Intermediate Water

Latitudinal body-mass trends in Oligo-Miocene mammals

Paleobiology ◽  
2016 ◽  
Vol 42 (4) ◽  
pp. 643-658
Author(s):  
John D. Orcutt ◽  
Samantha S. B. Hopkins
Keyword(s):  
Body Size ◽  
Body Mass ◽  
Regional Scale ◽  
Latitudinal Gradients ◽  
Bergmann’S Rule ◽  
Strongly Correlated ◽  
Bergmann's Rule ◽  
Deep Time ◽  
Causal Factors ◽  
Primary Driver

AbstractPaleecological data allow not only the study of trends along deep-time chronological transects but can also be used to reconstruct ecological gradients through time, which can help identify causal factors that may be strongly correlated in modern ecosystems. We have applied such an analysis to Bergmann’s rule, which posits a causal relationship between temperature and body size in mammals. Bergmann’s rule predicts that latitudinal gradients should exist during any interval of time, with larger taxa toward the poles and smaller taxa toward the equator. It also predicts that the strength of these gradients should vary with time, becoming weaker during warmer periods and stronger during colder conditions. We tested these predictions by reconstructing body-mass trends within canid and equid genera at different intervals of the Oligo-Miocene along the West Coast of North America. To allow for comparisons with modern taxa, body mass was reconstructed along the same transect for modernCanisandOdocoileus. Of the 17 fossil genera analyzed, only two showed the expected positive relationship with latitude, nor was there consistent evidence for a relationship between paleotemperature and body mass. Likewise, the strength of body-size gradients does not change predictably with climate through time. The evidence for clear gradients is ambiguous even in the modern genera analyzed. These results suggest that, counter to Bergmann’s rule, temperature alone is not a primary driver of body size and underscore the importance of regional-scale paleoecological analyses in identifying such drivers.

scholarly journals Soil Microbial Biogeography in a Changing World: Recent Advances and Future Perspectives

mSystems ◽  
2020 ◽  
Vol 5 (2) ◽  
Author(s):  
Haiyan Chu ◽  
Gui-Feng Gao ◽  
Yuying Ma ◽  
Kunkun Fan ◽  
Manuel Delgado-Baquerizo
Keyword(s):  
Microbial Communities ◽  
Soil Microbial Communities ◽  
Well Being ◽  
Ecosystem Functions ◽  
Soil Microbial ◽  
Microbial Biogeography ◽  
Recent Advances ◽  
Technological Advances ◽  
Global Change Scenarios ◽  
Changing World

ABSTRACT Soil microbial communities are fundamental to maintaining key soil processes associated with litter decomposition, nutrient cycling, and plant productivity and are thus integral to human well-being. Recent technological advances have exponentially increased our knowledge concerning the global ecological distributions of microbial communities across space and time and have provided evidence for their contribution to ecosystem functions. However, major knowledge gaps in soil biogeography remain to be addressed over the coming years as technology and research questions continue to evolve. In this minireview, we state recent advances and future directions in the study of soil microbial biogeography and discuss the need for a clearer concept of microbial species, projections of soil microbial distributions toward future global change scenarios, and the importance of embracing culture and isolation approaches to determine microbial functional profiles. This knowledge will be critical to better predict ecosystem functions in a changing world.

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