Diversity and Biogeography of Bathyal and Abyssal Seafloor Bacteria and Archaea Along a Mediterranean—Atlantic Gradient

Seafloor sediments cover the majority of planet Earth and microorganisms inhabiting these environments play a central role in marine biogeochemical cycles. Yet, description of the biogeography and distribution of sedimentary microbial life is still too sparse to evaluate the relative contribution of processes driving this distribution, such as the levels of drift, connectivity, and specialization. To address this question, we analyzed 210 archaeal and bacterial metabarcoding libraries from a standardized and horizon-resolved collection of sediment samples from 18 stations along a longitudinal gradient from the eastern Mediterranean to the western Atlantic. Overall, we found that biogeographic patterns depended on the scale considered: while at local scale the selective influence of contemporary environmental conditions appeared strongest, the heritage of historic processes through dispersal limitation and drift became more apparent at regional scale, and ended up superseding contemporary influences at inter-regional scale. When looking at environmental factors, the structure of microbial communities was correlated primarily with water depth, with a clear transition between 800 and 1,200 meters below sea level. Oceanic basin, water temperature, and sediment depth were other important explanatory parameters of community structure. Finally, we propose increasing dispersal limitation and ecological drift with sediment depth as a probable factor for the enhanced divergence of deeper horizons communities.

Integrating Effects of Source-Dependent Factors on Sediment-Depth Scaling of Additional Site Amplification to Ground-Motion Prediction Equation

ABSTRACT It is crucial to include additional site amplification effects resulting from the thick sediment on ground motions in the reliable assessment for seismic hazard in sedimentary basins. Ground-motion residual analysis with respect to ground-motion prediction equation is performed to evaluate additional site amplifications at over 200 K-NET stations within and around Kanto basin. We first investigate the potential effects on additional site amplifications resulted from the sediment depth and several source-dependent factors. Results reveal that source-to-site distance, focal depth, and source azimuth all have nonnegligible effects on additional site amplifications, especially the focal depth. Thick sedimentary sites amplify long-period ground motions from distant earthquakes more strongly than those from local earthquakes. Ground motions from shallow crustal earthquakes generally experience much stronger amplifications than those from those deep subduction earthquakes, much more predominant for long-period ground motions (>1.0 s) at thick sedimentary sites. Meanwhile, we develop the empirical model after integrating contributions from sediment depth, source-to-site distance, and focal depth for predicting additional site amplification effects. Considering the typical case of the distant shallow crustal earthquakes, additional site amplifications at thick sedimentary sites within Kanto basin generally show an increasing trend with the oscillation period increased, whereas they are generally characterized by a decreasing trend at shallow sedimentary sites outside the basin. The mean additional site amplification is up to about 2.0 within Kanto basin, whereas 0.5–0.65 outside Kanto basin, for ground motions at oscillation periods of 2.0–5.0 s. Mean amplifications within Kanto basin are about 3.5 times larger than those outside the basin for long-period ground motions at 2.0–5.0 s. Sites northeast to Kanto basin show the largest amplifications up to about 3.0 at periods of 0.15 and 5.0 s, which may be resulted from the basin edge effects.

16S and 18S rRNA Gene Metabarcoding Provide Congruent Information on the Responses of Sediment Communities to Eutrophication

Metabarcoding analyses of bacterial and eukaryotic communities have been proposed as efficient tools for environmental impact assessment. It has been unclear, however, to which extent these analyses can provide similar or differing information on the ecological status of the environment. Here, we used 16S and 18S rRNA gene metabarcoding to compare eutrophication-induced shifts in sediment bacterial and eukaryotic community structure in relation to a range of porewater, sediment and bottom-water geochemical variables, using data obtained from six stations near a former rainbow trout farm in the Archipelago Sea (Baltic Sea). Shifts in the structure of both community types were correlated with a shared set of variables, including porewater ammonium concentrations and the sediment depth-integrated oxygen consumption rate. Distance-based redundancy analyses showed that variables typically employed in impact assessments, such as bottom water nutrient concentrations, explained less of the variance in community structure than alternative variables (e.g., porewater NH4+ inventories and sediment depth-integrated O2 consumption rates) selected due to their low collinearity (up to 40 vs. 58% of the variance explained, respectively). In monitoring surveys where analyses of both bacterial and eukaryotic communities may be impossible, either 16S or 18S rRNA gene metabarcoding can serve as reliable indicators of wider ecological impacts of eutrophication.

Analytical representations of the Residence Time Distribution (RTD) associated with Hyporheic Exchange beneath Dune-like bedforms at different sediment bed depths

The hyporheic exchange below dune-shaped bedforms has a great impact on the stream environment. One of the most important properties of the hyporheic zone is the residence time distribution (RTD) of flow paths in the sediment domain. Here we evaluate the influence of an impervious layer, at a dimensionless sediment depth of db*=2πdbλ where λ is the dune wavelength, on the form of the hyporheic exchange RTD. Empirical RTDs were generated, over a range of db*values, from numerical particle tracking experiments in which 10000 particles sinusoidally distributed over a flatbed domain were released. These empirical RTDs are best represented by the Gamma, Log-Normal and Fréchet distributions over normalized bed depth of 0<=db*≤1.2,1.2<db*≤3.1, and db*>3.1, respectively. The depth dependence of the analytical distribution parameters is also presented, together with a set of regression formulae to predict these parameters based on db*with a high degree of accuracy (R2>99.8%). These results contribute to our understanding of the physical and mixing processes underpinning hyporheic exchange in streams and allow for a quick evaluation of its likely impact on nutrient and contaminant processing (e.g., based on the magnitude of the Damköhler number). Keywords: Dunes, bedforms, residence times distribution, sediment depth effect, Hyporheic residence times, analytical representation, two parametric distributions, Damköhler Number.

Radiocarbon dating of individual foram tests show that alleged Lessepsian species are of Holocene age

&lt;p&gt;The Lessepsian invasion &amp;#8211; the largest marine biological invasion &amp;#8211; followed the opening of the Suez Canal in 1869 (81 years BP). Shortly afterwards, tropical species also distributed in the Red Sea appeared on Mediterranean shores: it was the dawn of what would become the invasion of several hundred tropical species. The time of the Suez Canal opening coincided with an acceleration in natural history exploration and description, but the eastern sectors of the Mediterranean Sea lagged behind and were thoroughly explored only in the second half of the 20&lt;sup&gt;th&lt;/sup&gt; century. Many parts are still insufficiently studied today. Baseline information on pre-Lessepsian ecosystem states is thus scarce. This knowledge gap has rarely been considered by invasion scientists: every new finding of species belonging to tropical clades has been assumed to be a Lessepsian invader.&lt;/p&gt;&lt;p&gt;We here question this assumption by radiocarbon dating seven individual tests of miliolids &amp;#8211; imperforated calcareous foraminifera &amp;#8211; belonging to five alleged non-indigenous species. Tests were found in two sediment cores collected at 30 and 40 m depth off Ashqelon, on the Mediterranean Israeli shelf. We dated one &lt;em&gt;Cribromiliolinella milletti &lt;/em&gt;(core at 40 m, 20 cm sediment depth), three &lt;em&gt;Nodophthalmidium antillarum &lt;/em&gt;(core at 40 m, 35 cm sediment depth), one &lt;em&gt;Miliolinella &lt;/em&gt;cf. &lt;em&gt;fichteliana &lt;/em&gt;(core at 30 m, 110 cm sediment depth), one &lt;em&gt;Articulina alticostata &lt;/em&gt;(core at 40 m, 35 cm sediment depth) and one &lt;em&gt;Spiroloculina antillarum &lt;/em&gt;(core at 30 m, 110 cm sediment depth). All foraminiferal tests proved to be of Holocene age, with a median calibrated age spanning between 749 and 8285 years BP. Only one test of &lt;em&gt;N. antillarum&lt;/em&gt; showed a 2-sigma error overlapping the time of the opening of the Suez Canal, but with a median age of 1123 years BP. Additionally, a thorough literature search resulted in a further record of &lt;em&gt;S. antillarum&lt;/em&gt; in a core interval dated 1820&amp;#8211;2064 years BP in Turkey.&lt;/p&gt;&lt;p&gt;Therefore, these foraminiferal species are not introduced, but native species. They are all circumtropical or Indo-Pacific and in the Mediterranean distributed mostly in the eastern sectors (only &lt;em&gt;S. antillarum&lt;/em&gt; occurs also in the Adriatic Sea). Two hypotheses can explain our results: these species are Tethyan relicts that survived the Messinian salinity crisis (5.97&amp;#8211;5.33 Ma) and the glacial periods of the Pleistocene in the Eastern Mediterranean, which may have never desiccated completely during the Messinian crisis and which may have worked as a warm-water refugium in the Pleistocene; or they entered the Mediterranean Sea from the Red Sea more recently but before the opening of the Suez Canal, for example during the Last Interglacial (MIS5e) high-stand (125,000 years BP) when the flooded Isthmus of Suez enabled exchanges between the Mediterranean and the Indo-Pacific fauna. The recognition that some alleged Lessepsian invaders are in fact native species influences our understanding of the invasion process, its rates and environmental correlates.&lt;/p&gt;

Estimation Model of Mangrove Carbon Stock Using LDCM Imagery

Mangroves are one of the forest ecosystems with the capacity to reduce greenhouse effect. However, there is limited data on thecarbon absorbent properties, and, a fast as well as accurate method of estimating the stock in mangrove is needed. The objective of this research, therefore, was to obtain an estimation model of mangrove carbon stocks, using LDCM satellite imagery. Thisdevelopment involved a hybrid method,where information obtainedfrom LDCM satellite imagery were combined with the field data. The result of this studyidentified the best model to estimate carbon stock. This involvedthe combination of total vegetation stock, using the VARI vegetation index (power regression/ geometry) and soil composition, basedon six variables multiple regression.The%RMSE test result was determined to be 9.58%. In addition, field data was not required in modelsinvolving two variables (MSAVI vegetation index and average sediment depth 100.6 cm), and the % RMSE determined was 34.18%.

Species composition and habitat preferences of benthic ostracod and foraminifera in seagrass and non-seagrass systems within a tropical estuary

Ostracods and foraminifera are excellent indicators of environmental change and can act as proxies for the presence of seagrass meadows. These proxies have been under-utilized in vulnerable coastal ecosystems in South-east Asia, and the fundamental habitat and environmental parameters required for such application in environmental monitoring have not yet been established. We investigated the habitat preferences of ostracods and foraminiferal species in seagrass and non-seagrass habitats within Sungai Pulai Estuary (Johor, Malaysia), a system currently undergoing major coastal changes. Samples consisted of surficial and downcore sediments collected from two seagrass meadows and a non-seagrass habitat. Multivariate analysis determined the variations in spatial and depth distribution of the meiofauna. Species dominance, abundance and distribution varied between sites, whereas diversity and community structure varied with sediment depth. We found fewer ostracod individuals (N = 1133) than foraminifera (N = 7242). Ostracods were more species-diverse (H′ = 3.34) in the non-vegetated area compared with seagrass areas (H′ = 2.74), whereas foraminifera species were most diverse (H′ = 3.60) in seagrass areas. Opportunistic species, such as Loxoconcha lilljeborgii, Asterorotalia pulchella, Murrayinella globosa, Ammonia tepida and Elphidium neosimplex dominated the meiofaunal assemblages. The presence of Nummulitidae and Paracyprididae in downcore samples provided information related to rare species and families. Salinity, organic matter and percentage of sand explained much of the meiofaunal distribution. Our findings provide new insight into the factors influencing the presence and distribution of ostracods and foraminifera in the estuary, comprising baseline information for understanding the vulnerability of such habitats to anthropogenic changes.

The critical role of pore size on depth-dependent microbial cell counts in sediments

Cell counts decrease with sediment depth. Typical explanations consider limiting factors such as water availability and chemistry, carbon source, nutrients, energy and temperature, and overlook the role of pore size. Our analyses consider sediment self-compaction, the evolution of pore size with depth, and the probability of pores larger than the microbial size to compute the volume fraction of life-compatible pores. We evaluate cell counts vs. depth profiles gathered at 116 sites worldwide. Results confirm the critical role of pore size on cell counts in the subsurface and explain much of the data spread (from ~ 9 orders of magnitude range in cell counts to ~ 2 orders). Cells colonize pores often forming dense biofilms, thus, cell counts in pores are orders of magnitude higher than in the water column. Similar arguments apply to rocks.