Mechanisms of summer intraseasonal sea surface temperature oscillations in the Bay of Bengal

Intraseasonal variations (ISV) of sea surface temperature (SST) in the Bay of Bengal (BoB) is highest in its northwestern part. An Indian Ocean model forced by QuikSCAT winds and climatological river discharge (QR run) reproduces ISV of SST, albeit with weaker magnitude. Air-sea fluxes, in the presence of a shallow mixed layer, efficiently effect intraseasonal SST fluctuations. Warming during intraseasonal events is smaller (<1°C) for June - July period and larger (1.5° to 2°C) during September, the latter due to a thinner mixed layer. To examine the effect of salinity on ISV, the model was run by artificially increasing the salinity (NORR run) and by decreasing it (MAHA10 run). In NORR, both rainfall and river discharge were switched off and in MAHA10 the discharge by river Mahanadi was increased tenfold. The spatial pattern of ISV as well as its periodicity was similar in QR, NORR and MAHA10. The ISV was stronger in NORR and weaker in MAHA10, compared to QR. In NORR, both intraseasonal warming and cooling were higher than in QR, the former due to reduced air-sea heat loss as the mean SST was lower, and the latter due to enhanced subsurface processes resulting from weaker stratification. In MAHA10, both warming and cooling were lower than in QR, the former due to higher air-sea heat loss owing to higher mean SST, and the latter due to weak subsurface processes resulting from stronger stratification. These model experiments suggest that salinity effects are crucial in determining amplitudes of intraseasonal SST variations in the BoB.

Under-representation of intrinsic terminators across bacterial genomic islands: Rho as a principal regulator of xenogenic DNA expression

Two transcription termination mechanisms - intrinsic and Rho-dependent - have evolved in bacteria. The Rho factor occurs in most bacterial lineages, and has been hypothesized to play a global regulatory role. Genome-wide studies using microarray, 2D-gel electrophoresis and ChIP-chip provided evidence that Rho serves to silence transcription from horizontally acquired genes and prophages in Escherichia coli K-12, implicating the factor to be a part of the ``cellular immune mechanism'' protecting against deleterious phages and aberrant gene expression from acquired xenogenic DNA. We have investigated this model by adopting an alternate in silico approach and have extended the study to other species. Our analysis shows that several genomic islands across diverse phyla have under-representation of intrinsic terminators, similar to that experimentally observed in E. coli K-12. This implies that Rho-dependent termination is the predominant process operational in these islands and that silencing of foreign DNA is a conserved function of Rho. From the present analysis, it is evident that horizontally acquired islands have lost intrinsic terminators to facilitate Rho-dependent termination. These results underscore the importance of Rho as a conserved, genome-wide sentinel that regulates potentially toxic xenogenic DNA. (C) 2012 Elsevier B.V. All rights reserved.

Signatures of Indian ocean Dipole and El Nino-Southern Oscillation events in sea level variations in the Bay of Bengal

We investigate the impact of the Indian Ocean Dipole (IOD) and El Nino and the Southern Oscillation (ENSO) on sea level variations in the North Indian Ocean during 1957-2008. Using tide-gauge and altimeter data, we show that IOD and ENSO leave characteristic signatures in the sea level anomalies (SLAs) in the Bay of Bengal. During a positive IOD event, negative SLAs are observed during April-December, with the SLAs decreasing continuously to a peak during September-November. During El Nino, negative SLAs are observed twice (April-December and November-July), with a relaxation between the two peaks. SLA signatures during negative IOD and La Nina events are much weaker. We use a linear, continuously stratified model of the Indian Ocean to simulate their sea level patterns of IOD and ENSO events. We then separate solutions into parts that correspond to specific processes: coastal alongshore winds, remote forcing from the equator via reflected Rossby waves, and direct forcing by interior winds within the bay. During pure IOD events, the SLAs are forced both from the equator and by direct wind forcing. During ENSO events, they are primarily equatorially forced, with only a minor contribution from direct wind forcing. Using a lead/lag covariance analysis between the Nino-3.4 SST index and Indian Ocean wind stress, we derive a composite wind field for a typical El Nino event: the resulting solution has two negative SLA peaks. The IOD and ENSO signatures are not evident off the west coast of India.

Ganga-Brahmaputra river discharge from Jason-2 radar altimetry: An update to the long-term satellite-derived estimates of continental freshwater forcing flux into the Bay of Bengal

This paper discusses the use of Jason-2 radar altimeter measurements to estimate the Ganga-Brahmaputra surface freshwater flux into the Bay of Bengal for the period mid-2008 to December 2011. A previous estimate was generated for 1993-2008 using TOPEX-Poseidon, ERS-2 and ENVISAT, and is now extended using Jason-2. To take full advantages of the new availability of in situ rating curves, the processing scheme is adapted and the adjustments of the methodology are discussed here. First, using a large sample of in situ river height measurements, we estimate the standard error of Jason-2-derived water levels over the Ganga and the Brahmaputra to be respectively of 0.28 m and 0.19 m, or less than similar to 4% of the annual peak-to-peak variations of these two rivers. Using the in situ rating curves between water levels and river discharges, we show that Jason-2 accurately infers Ganga and Brahmaputra instantaneous discharges for 2008-2011 with mean errors ranging from similar to 2180 m(3)/s (6.5%) over the Brahmaputra to similar to 1458 m(3)/s (13%) over the Ganga. The combined Ganga-Brahmaputra monthly discharges meet the requirements of acceptable accuracy (15-20%) with a mean error of similar to 16% for 2009-2011 and similar to 17% for 1993-2011. The Ganga-Brahmaputra monthly discharge at the river mouths is then presented, showing a marked interannual variability with a standard deviation of similar to 12500 m(3)/s, much larger than the data set uncertainty. Finally, using in situ sea surface salinity observations, we illustrate the possible impact of extreme continental freshwater discharge event on the northern Bay of Bengal as observed in 2008.

Shola habitats on sky islands: status of research on montane forests and grasslands in southern India

The Shola habitat on the high elevation sky islands of the Western Ghats in southern India is a unique habitat. Although this habitat hosts a disproportionately high level of endemism and is threatened by anthropogenic modifications, it has received little research attention. We compiled publications of research conducted in this habitat from scientific databases and the grey literature to examine trends in publication. For a quantitative summary, all publications were classified according to the taxa of research and the broad topic of research. We identified 279 publications from 1964 and found an almost threefold increase in the number of publications and diversity of research topics studied over the last decade. Studies on flora, birds and mammals have been numerous (62% of the studies examined), but certain taxa like fish (1%) have been ignored. Most studies (65%) are descriptive, focusing on diversity, distribution trends and management suggestions, while surprisingly few have concentrated on climate change, ecological restoration and invasive species, all major threats to this landscape. We have identified some key gaps in research and conservation focus that future studies could address. We also suggest that initiatives like edited volumes and special journal sections, along with the use of creative commons licensed data-sharing portals, can be used to usher unpublished work into the public domain.

A summer monsoon pump to keep the Bay of Bengal salty

The Bay of Bengal receives a large influx of freshwater from precipitation and river discharge. Outflow of excess freshwater and inflow of saltier water is required to prevent the bay from freshening. Relatively fresh water flows out of the bay along its boundaries and inflow of saltier water occurs via the Summer Monsoon Current (SMC), which flows eastward from the Arabian Sea into the bay. This saltier water, however, slides under the lighter surface water of the bay. Maintaining the salt balance of the bay therefore demands upward mixing of this saltier, subsurface water. Here, we show that an efficient mechanism for this mixing is provided by upward pumping of saltier water in several bursts during the summer monsoon along the meandering path of the SMC. Advection by currents can then take this saltier water into the rest of the basin, allowing the bay to stay salty despite a large net freshwater input.

Flying between Sky Islands: The Effect of Naturally Fragmented Habitat on Butterfly Population Structure

High elevation montane areas are called ``sky islands'' when they occur as a series of high mountains separated by lowland valleys. Different climatic conditions at high elevations makes sky islands a specialized type of habitat, rendering them naturally fragmented compared to more continuous habitat at lower elevations. Species in sky islands face unsuitable climate in the intervening valleys when moving from one montane area to another. The high elevation shola-grassland mosaic in the Western Ghats of southern India form one such sky island complex. The fragmented patches make this area ideal to study the effect of the spatial orientation of suitable habitat patches on population genetic structure of species found in these areas. Past studies have suggested that sky islands tend to have genetically structured populations, possibly due to reduced gene flow between montane areas. To test this hypothesis, we adopted the comparative approach. Using Amplified Fragment Length Polymorphisms, we compared population genetic structures of two closely related, similar sized butterfly species: Heteropsis oculus, a high elevation shola-grassland specialist restricted to the southern Western Ghats, and Mycalesis patnia, found more continuously distributed in lower elevations. In all analyses, as per expectation the sky island specialist H. oculus exhibited a greater degree of population genetic structure than M. patnia, implying a difference in geneflow. This difference in geneflow in turn appears to be due to the natural fragmentation of the sky island complexes. Detailed analysis of a subset of H. oculus samples from one sky island complex (the Anamalais) showed a surprising genetic break. A possible reason for this break could be unsuitable conditions of higher temperature and lower rainfall in the intervening valley region. Thus, sky island species are not only restricted by lack of habitat continuity between montane areas, but also by the nature of the intervening habitat.

On the nature of meandering of the springtime western boundary current in the Bay of Bengal

We present evidence that the springtime western boundary current (WBC) in the Bay of Bengal is a continuous northward-flowing current from about 12 degrees N to 17 degrees N, which then separates from the coast at around 18 degrees N. We first revisit a hydrographic data set collected in 1987 from a potential vorticity perspective, and then analyze absolute dynamic height maps from satellite altimeters during the period 2000-2010. The altimetric maps suggest that the mean configuration of the WBC is that of an intense current with two anticyclonic eddies on the offshore side, which are part of the basin-wide anticyclonic circulation. The WBC consistently separates from the coast at around 18 degrees N in all years between 2000 and 2010. The path of the eastward-flowing mean stream after separation appears to be consistent with isolines of f/H and with Ertel's potential vorticity, based on an analysis of the hydrographic data from 1987.

The upper Bay of Bengal salinity structure in a high-resolution model

Salinity in the Bay of Bengal is highly heterogeneous, with extremely fresh waters found at the surface in the Northern part of the basin, and saltier waters at subsurface as well as to the south. This paper investigates the seasonal structure of sea surface salinity of the Bay in a regional high-resolution model forced by ERA-Interim reanalysis and various precipitation products. Surface circulation is believed to drive the spreading of northern Bay of Bengal fresh waters to the rest of the Indian Ocean. We first present a series of experiments to infer the sensitivity of modeled circulation to various numerical choices. Surface circulation is found to be sensitive to the horizontal resolution of the model, with the 1/12 degrees version appearing much more realistic than the 1/4 degrees version. The sidewall boundary condition is also drastically influencing the characteristics of the western boundary current simulated. We then investigate the sensitivity of the salinity response to the various precipitation products. We observe that ERA-Interim excess precipitation induces a fresh bias in the surface salinity response. Spaceborne precipitation products are more satisfactory. We then identify the pathways of the northern Bay freshwater mass, based on passive tracers experiments. Our model suggests that over timescales of a few months, vertical exchanges between the upper fresh layer and the underlying saltier layer appear to be the main export pathway for the freshwater. The horizontal circulation within the mixed layer also acts to convey fresh waters out of the Bay at these timescales, but in a lesser quantity compared to the vertical export. Beyond its intrinsic interest for the understanding of Bay of Bengal physics, this study highlights the need for a careful design of any realistic numerical model, in three key aspects: the choice of the resolution of the model, the choice of the sub-grid scale parameterizations, and the choice of the forcing fluxes. (C) 2013 Elsevier Ltd. All rights reserved.

Slow Slip Acceleration beneath Andaman Islands Triggered by the 11 April 2012 Indian Ocean Earthquakes

The M-w 8.6 and 8.2 strike-slip earthquakes that struck the northeast Indian Ocean on 11 April 2012 resulted in coseismic deformation both at near and distant sites. The slip distribution, deduced using seismic-wave analysis for the orthogonal faults that ruptured during these earthquakes, is sufficient to predict the coseismic displacements at the Global Positioning System (GPS) sites, such as NTUS, PALK, and CUSV, but fall short at four continuous sites in the Andaman Islands region. Slip modeling, for times prior to the events, suggests that the lower portion of the thrust fault beneath the Andaman Islands has been slipping at least at the rate of 40 cm/yr, in response to the 2004 Sumatra-Andaman coseismic stress change. Modeling of GPS displacements suggests that the en echelon and orthogonal fault ruptures of the 2012 intraplate oceanic earthquakes could have possibly accelerated the ongoing slow slip, along the lower portion of the thrust fault beneath the islands with a month-long slip of 4-10 cm. The misfit to the coseismic GPS displacements along the Andaman Islands could be improved with a better source model, assuming that no local process contributed to this anomaly.

A modeling study of the processes of surface salinity seasonal cycle in the Bay of Bengal

In response to the Indian Monsoon freshwater forcing, the Bay of Bengal exhibits a very strong seasonal cycle in sea surface salinity (SSS), especially near the mouths of the Ganges-Brahmaputra and along the east coast of India. In this paper, we use an eddy-permitting (similar to 25 km resolution) regional ocean general circulation model simulation to quantify the processes responsible for this SSS seasonal cycle. Despite the absence of relaxation toward observations, the model reproduces the main features of the observed SSS seasonal cycle, with freshest water in the northeastern Bay, particularly during and after the monsoon. The model also displays an intense and shallow freshening signal in a narrow (similar to 100 km wide) strip that hugs the east coast of India, from September to January, in good agreement with high-resolution measurements along two ships of opportunity lines. The mixed layer salt budget confirms that the strong freshening in the northern Bay during the monsoon results from the Ganges-Brahmaputra river discharge and from precipitation over the ocean. From September onward, the East India Coastal Current transports this freshwater southward along the east coast of India, reaching the southern tip of India in November. The surface freshening results in an enhanced vertical salinity gradient that increases salinity of the surface layer by vertical processes. Our results reveal that the erosion of the freshwater tongue along the east coast of India is not driven by northward horizontal advection, but by vertical processes that eventually overcome the freshening by southward advection and restore SSS to its premonsoon values. The salinity-stratified barrier layer hence only acts as a ``barrier'' for vertical heat fluxes, but is associated with intense vertical salt fluxes in the Bay of Bengal.

Interactome analyses of Salmonella pathogenicity islands reveal SicA indispensable for virulence

Background: Serovars of Salmonella enterica, namely Typhi and Typhimurium, reportedly, are the bacterial pathogens causing systemic infections like gastroenteritis and typhoid fever. To elucidate the role and importance in such infection, the proteins of the Type III secretion system of Salmonella pathogenicity islands and two component signal transduction systems, have been mainly focused. However, the most indispensable of these virulent ones and their hierarchical role has not yet been studied extensively. Results: We have adopted a theoretical approach to build an interactome comprising the proteins from the Salmonella pathogeneicity islands (SPI) and two component signal transduction systems. This interactome was then analyzed by using network parameters like centrality and k-core measures. An initial step to capture the fingerprint of the core network resulted in a set of proteins which are involved in the process of invasion and colonization, thereby becoming more important in the process of infection. These proteins pertained to the Inv, Org, Prg, Sip, Spa, Ssa and Sse operons along with chaperone protein SicA. Amongst them, SicA was figured out to be the most indispensable protein from different network parametric analyses. Subsequently, the gene expression levels of all these theoretically identified important proteins were confirmed by microarray data analysis. Finally, we have proposed a hierarchy of the proteins involved in the total infection process. This theoretical approach is the first of its kind to figure out potential virulence determinants encoded by SPI for therapeutic targets for enteric infection. Conclusions: A set of responsible virulent proteins was identified and the expression level of their genes was validated by using independent, published microarray data. The result was a targeted set of proteins that could serve as sensitive predictors and form the foundation for a series of trials in the wet-lab setting. Understanding these regulatory and virulent proteins would provide insight into conditions which are encountered by this intracellular enteric pathogen during the course of infection. This would further contribute in identifying novel targets for antimicrobial agents. (C) 2014 Elsevier Ltd. All rights reserved.

Impact of diurnal forcing on intraseasonal sea surface temperature oscillations in the Bay of Bengal

The diurnal cycle is an important mode of sea surface temperature (SST) variability in tropical oceans, influencing air-sea interaction and climate variability. Upper ocean mixing mechanisms are significant at diurnal time scales controlling the intraseasonal variability (ISV) of SST. Sensitivity experiments using an Ocean General Circulation Model (OGCM) for the summer monsoon of the year 2007 show that incorporation of diurnal cycle in the model atmospheric forcings improves the SST simulation at both intraseasonal and shorter time scales in the Bay of Bengal (BoB). The increase in SST-ISV amplitudes with diurnal forcing is approximate to 0.05 degrees C in the southern bay while it is approximate to 0.02 degrees C in the northern bay. Increased intraseasonal warming with diurnal forcing results from the increase in mixed layer heat gain from insolation, due to shoaling of the daytime mixed layer. Amplified intraseasonal cooling is dominantly controlled by the strengthening of subsurface processes owing to the nocturnal deepening of mixed layer. In the southern bay, intraseasonal variability is mainly determined by the diurnal cycle in insolation, while in the northern bay, diurnal cycle in insolation and winds have comparable contributions. Temperature inversions (TI) develop in the northern bay in the absence of diurnal variability in wind stress. In the northern bay, SST-ISV amplification is not as large as that in the southern bay due to the weaker diurnal variability of mixed layer depth (MLD) limited by salinity stratification. Diurnal variability of model MLD is not sufficient to create large modifications in mixed layer heat budget and SST-ISV in the northern bay.

Phytoplankton size structure in the southern Bay of Bengal modified by the Summer Monsoon Current and associated eddies: Implications on the vertical biogenic flux

The present study combines field and satellite observations to investigate how hydrographical transformations influence phytoplankton size structure in the southern Bay of Bengal during the peak Southwest Monsoon/Summer Monsoon (July-August). The intrusion of the Summer Monsoon Current (SMC) into the Bay of Bengal and associated changes in sea surface chemistry, traceable eastward up to 90 degrees E along 8 degrees N, seems to influence biology of the region significantly. Both in situ and satellite (MODIS) data revealed low surface chlorophyll except in the area influenced by the SMC During the study period, two well-developed cydonic eddies (north) and an anti-cyclonic eddy (south), closely linked to the main eastward flow of the SMC, were sampled. Considering the capping effect of the low-saline surface water that is characteristic of the Bay of Bengal, the impact of the cyclonic eddy, estimated in terms of enhanced nutrients and chlorophyll, was mostly restricted to the subsurface waters (below 20 m depth). Conversely, the anti-cyclonic eddy aided by the SMC was characterized by considerably higher nutrient concentration and chlorophyll in the upper water column (upper 60 m), which was contrary to the general characteristic of such eddies. Albeit smaller phytoplankton predominated the southern Bay of Bengal (60-95% of the total chlorophyll), the contribution of large phytoplankton was double in the regions influenced by the SMC and associated eddies. Multivariate analysis revealed the extent to which SMC-associated eddies spatially influence phytoplankton community structure. The study presents the first direct quantification of the size structure of phytoplankton from the southern Bay of Bengal and demonstrates that the SMC-associated hydrographical ramifications significantly increase the phytoplankton biomass contributed by larger phytoplankton and thereby influence the vertical opal and organic carbon flux in the region. (C) 2014 Elsevier B.V. All rights reserved.