Comprehensive understanding and quantification of different aspects of estuarine carbon (C) cycle are essential to decipher regional and global changes. Here, premonsoon C biogeochemistry of two ...contrasting estuarine systems (Hooghly - anthropogenically influenced and Sundarbans - mangrove dominated) located in the deltaic region of Ganges, India, has been investigated. The Hooghly showed sharper salinity gradient (0.48–32.94) and wider pH range (7.56–8.25) compared to the Sundarbans (salinity: 27.22–29.82; pH: 8.16–8.31). The DIC concentration in the Hooghly (2.27 ± 0.22 mmol L
−1
) was higher than the Sundarbans (1.77 ± 0.06 mmol L
−1
) with relatively depleted δ
13
C
DIC
. The mixing model analysis suggested DIC chemistry in the Hooghly to be principally regulated by respiration of estuarine algae, whereas Sundarbans showed evidences for DIC removal and mangrove-derived DIC contribution. The DOC behaved non-conservatively in both the estuaries. The POC in the Hooghly showed signatures of estuarine algae and marine plankton in the mixing and marine zones, whereas dominance of terrestrial organic matter was found in the freshwater zone of the Hooghly and estuaries of Sundarbans. Both
p
CO
2
(556–5002 μatm) and CH
4
(15.4–445.7 nmol L
−1
) varied over a wider range in the Hooghly compared to the Sundarbans (
p
CO
2
: 268–418 μatm; CH
4
: 41.6–71.5 nmol L
−1
). The Sundarbans acted as a net sink for CO
2
, whereas the Hooghly was a significant source to the regional atmosphere. Both the estuaries acted as source of CH
4
with comparable exchange fluxes. Overall, the Sundarbans was a net C sink and the Hooghly was a net source to regional atmosphere via cumulative fluxes of CO
2
and CH
4
.
•This study is focused on the understanding distribution of nutrients in the Eastern Equatorial Indian Ocean, their significance on biogeochemical cycles and the impact of water masses on ...nutrients.•The nutrient maxima were recorded at shallower depths.•EEIO surface water was found to be oligotrophic with bio-limiting nitrogen.•An excess of phosphate over nitrate was found between 50-100m depth.•Shallow-depth mineralization was noticed in this region during the study.•Insignificant influence of Indonesian Through Flow (ITF) on nutrient values.•Allochthonous supply of organic matter comes through Indonesian Through Flow (ITF) influencing and augmenting nutrient regeneration.
The seasonal reversal of ocean circulation associated with seasonal change in the direction of prevailing winds and the occurrence of several anomalous events in the Eastern Equatorial Indian Ocean (EEIO) make this region dynamic and complex in terms of its biogeochemical characteristics. Two multidisciplinary cruises were conducted to measure nutrients and associated physicochemical parameters across the water column (up to 1000 m) of the EEIO during boreal summer and winter monsoons to understand the distribution of nutrients and their spatio-temporal variability from a biogeochemical perspective. The seasonality in the thermohaline structure of the region is indistinct except for surface salinity drop during summer monsoon due to more precipitation on-site and in adjoining areas. Low concentrations of chlorophyll at the surface and in the deep chlorophyll maxima represent the oligotrophic nature of this region. Surface water was found nutrient-depleted (0.03–0.4 µM Nitrate, 0.02–0.13 µM Phosphate). The maxima of vertical profiles of nitrate and phosphate were recorded at a shallower depth (150–200 m) when compared to its maxima in usual oceanic conditions, but a silicate maximum was recorded in deeper water. In the surface and upper mixed layer paucity of nutrients resulted in low N:P and N:Si ratios. Therefore, nitrogen limitation is evident. The overall ratio of N:P yielded a mean value of 15.33 and matched with the representative literature value for the Indian Ocean. The minimum oxygen values (<50 µM) in the deep water (150–200 m) indicated a hypoxic condition. No signature of denitrification and a moderate nitrate deficit were observed in deep waters. The negative values of Nitrate anomaly (N-tracer) at 50–100 m depth were attributed to a Watermass influenced by denitrification. The prevailing oligotrophic condition caused limited synthesis of organic matter and subsequently little decomposition in deep water. The maxima in the apparent oxygen utilization (AOU) profile are confined to 150 to 200 m depth and represent the most active zone for regeneration that is limited to shallow depth. Regenerated nutrients reached maxima at shallower depth and primarily control material cycling in this region. Supply of nitrate to the surface water based on the preformed values of prevailing water mass was primarily by Bay of Bengal water. According to the findings of this study, preformed nitrate concentrations between 100 and 200 metres below the surface were found very low, indicating that Indonesian Through Flow (ITF) has little impact on the distribution of nutrients in this area.
Tidal transport from coastal wetlands (“outwelling”), together with riverine fluxes, provide the most important sources of terrigenous organic matter (OM) to the ocean. The flux of dissolved organic ...carbon (DOC) from the mangrove swamps accounts for 10% of the terrestrial DOC flux to the coastal water. This study examines the sources, distribution, and export of dissolved OM at interannual, seasonal, and diurnal bases along the estuaries located at the Sundarbans, the world’s largest deltaic mangrove and heritage site. Sampling was carried out from the riverine (Hooghly) and mangrove-dominated tidal estuaries (Saptamukhi, Thakuran, Matla), covering all three seasons (pre-monsoon, monsoon, and post-monsoon) during 2012–2017. DOC varied at a broad range, from 109 to 462 μM (n = 146), with higher concentration observed in the Hooghly (383 ± 120 μM, n = 35) than the mangrove estuaries (246 ± 82 to 266 ± 120 μM, n = 111). Non-conservative mixing of DOC along the salinity gradient attested to mangrove input, particularly in the polyhaline waters. Upper and mid estuarine zones of the mangrove estuaries showed slightly higher DOC concentration (270 ± 92 μM, n = 84, salinity range 18–25) than in the mouth (250 ± 85 μM, n = 27, salinity range 26–27), because of the dilution with marine waters having low DOC concentration and shorter water residence time downstream. Seasonally, higher DOC concentration during the post-monsoon might be linked to higher litterfall, promoting leaching of organic compounds to the water. In that connection, colored dissolved organic matter (CDOM) could be a by-product of mangrove litter leaching, and its absorption coefficient (at 350 nm) exhibited non-conservative mixing pattern at wide ranges from 2.5 to 7.6 m−1 (n = 40). CDOM enrichment was observed in the surface water during the low tide when outwelling maximized. Overall, the central and eastern parts of the Indian Sundarbans showed enrichment of more terrigenous type CDOM (evident from optical proxies, e.g., S275–295 and SUVA254) than the western part, probably due to greater mangrove productivity in the eastern side. Flux estimates of DOM resulted in higher yield and export of mangrove-derived DOC but lower export of CDOM to the Bay of Bengal as compared to their riverine transport.
The world’s largest mangroves ecosystem, the Sundarbans, being highly productive and a place for extensive organic matter cycling, is considered to be the hotspot for biogeochemical studies in the ...tropical estuarine environment. Hence, the spatial and temporal dynamics of the biogenic gases (CO
2
, CH
4
, and N
2
O), also known as radiatively active gases, were measured in mangrove-dominated estuaries of the system. In addition to spatial and seasonal observation, three full tidal cycles were observed at one site. Results showed that the air/water gas saturations were widely distributed and highly variable along the stretch. The gas saturations showed varying responses to salinity and tidal fluctuations. This indicated that localized biogeochemical processes may be more influential than simple mixing and dilution processes in controlling the variability of these gases. The surface waters were always supersaturated with CH
4
(Up to 13,133%) relative to the atmosphere. However, N
2
O ranged from 8 to 1,286% and CO
2
from 30 to 2075%. N
2
O fluxes were ∼4.8 times higher in the pre-monsoon than the post-monsoon. CH
4
fluxes were ∼3.6 times higher in the pre-monsoon than both the monsoon and the post-monsoon. CO
2
fluxes were ∼10 times higher in the monsoon than both the pre-monsoon and the post-monsoon. The seasonality in the gas saturation could be linked more to the availability of substrates than physicochemical parameters. Overall, air/water CH
4
fluxes varied maximally (0.4–18.4 μmol m
−2
d
−1
), followed by CO
2
fluxes (−0.6–10.9 mmol m
−2
d
−1
), and N
2
O fluxes varied the least of all (−0.6–5.4 μmol m
−2
d
−1
). Interestingly, CH
4
and N
2
O fluxes were positively correlated to each other (
p
< 0.05), suggesting organic matter decomposition as the key factor in the production of these two gases. Finally, these water–air CO
2
, CH
4
, and N
2
O flux estimates show that the estuaries are a modest source of CH
4
but fluctuate between sources and sinks for CO
2
and N
2
O gases.
The large-scale protein-protein interaction (PPI) data has the potential to play a significant role in the endeavor of understanding cellular processes. However, the presence of a considerable ...fraction of false positives is a bottleneck in realizing this potential. There have been continuous efforts to utilize complementary resources for scoring confidence of PPIs in a manner that false positive interactions get a low confidence score. Gene Ontology (GO), a taxonomy of biological terms to represent the properties of gene products and their relations, has been widely used for this purpose. We utilize GO to introduce a new set of specificity measures: Relative Depth Specificity (RDS), Relative Node-based Specificity (RNS), and Relative Edge-based Specificity (RES), leading to a new family of similarity measures. We use these similarity measures to obtain a confidence score for each PPI. We evaluate the new measures using four different benchmarks. We show that all the three measures are quite effective. Notably, RNS and RES more effectively distinguish true PPIs from false positives than the existing alternatives. RES also shows a robust set-discriminating power and can be useful for protein functional clustering as well.
Nitrification is a vital biogeochemical process during which ammonium (NH
4
+
) is oxidized to nitrite (NO
2
−
) and nitrate (NO
3
−
) using oxygen. Nitrification is particularly important in ...estuaries, where nitrification rates have significant implications for ecosystem functioning. Our study investigated seasonal and spatial variations of nitrification rates in both water and sediment phases of mangrove ecosystems in the Indian Sundarbans, integrating the three major estuaries (Saptamukhi, Thakuran, and Matla). We used on board incubation to measure nitrifying activity i.e., ammonium oxidation rate (Ra) and nitrite oxidation rate (Rn) in the water column. We found that average Ra and Rn rates were similar, ranging from 31.1 to 31.8 nmol N L
−1
h
−1
, respectively. Water column nitrification rates showed an inverse relationship with salinity (
r
= − 0.51,
p
< 0.001), while substrate concentrations of ammonium had a direct impact on nitrification rates. Annual dissolved inorganic nitrogen (DIN) concentrations were 11.7 ± 7.65 µM, with an average nitrate (NO
3
−
) concentration of 4.5–16.3 µM and average ammonium (NH
4
+
) concentrations from 2.1 to 5 µM. Suspended particulate matter and chlorophyll showed positive (
r
= 0.38,
p
= 0.009) and negative (
r
= − 0.31,
p
= 0.034) correlations, respectively, with water column nitrification rates. For water, both Ra and Rn occurred at similar rates in our study area. In sediment, nitrifying activity (SEDn) rates ranged from 0.34 to 8.69 nmol N g wet wt
−1
h
−1
. SEDn showed positive and negative correlations with sediment temperature (temp) and pH, respectively. Based on our observations, the average water column nitrification potential ranged from 43 to 420 nmol N L
−1
h
−1
considering three estuaries, while the sediment nitrification potential estimated at Saptamukhi estuary showed a value of 69 nmol N g wet wt
−1
h
−1
.
We investigated diurnal-scale variations in the abundances of bacterioplankton, high and low nucleic acid (HNA, LNA) cells, and associated physico-chemical variables in a mangrove dominated estuary ...of the Indian Sundarbans, during pre-monsoon and monsoon conditions. Bacterioplankton abundance (BA) varying from 1.83 ± 0.47 to 0.34 ± 0.11 × 109 cells L−1 with lowest abundance during the monsoon, was mainly dominated by LNA cells (74.46 ± 12.79% to 74.36 ± 20.51%). In two time series studies bacterial productivity (BP), total bacterioplankton abundance and HNA cell numbers increased towards high tide (BA; 0.21–0.04 × 109 cells L−1, HNA; 0.11–0.06 × 109 cells L−1) while LNA cell abundance varied. Total bacterioplankton, HNA and LNA cell numbers were also highest during the night (total bacterioplankton; 0.32–0.04 × 109 cells L−1, HNA; 0.31–0.01 × 109 cells L−1, LNA; 0.01–0.03 × 109 cells L−1). Highest dissolved oxygen and pH was at high tide (high salinity), while other carbonate system parameters and dissolved inorganic nutrients (except DIP) were higher at low tide. The overall abundances of bacterioplankton, HNA and LNA cells were controlled by a combination of factors, water temperature and dissolved oxygen being the most important controls on day-night and tidal variation of bacterioplankton.
•Bacterioplankton is mainly dominated by LNA cells in mangrove water of Indian Sundarbans.•Abundance of bacterioplankton and HNA cells increase at high tide and night.•Bacterioplankton and sub-groups are regulated by multiple physico-chemical factors.
A detailed study on potential sources, variation, and environmental effects of the rainwater ions was carried out at Lothian Island, Sundarban mangrove forest, India, during the southwest monsoon ...(June–September) in 2019. On an event basis, the maximum rainwater precipitation was observed 17.65 mm Day
−1
and a minimum of 1.02 mm Day
−1
. The maximum amount of total precipitation was recorded in the month of July (237 mm). The volume weighted mean (VWM) concentration shows that the total ionic composition was 93.7 μeq L
−1
, whereas the percentage contribution of the total ionic concentration is found to be 45.97% to anions and 54.02% to the cations. Temporal variation was observed between early (June- July) and late monsoon (August—September), which shows a high concentration of major ions in early monsoon and low concentration in late monsoon due to the washout of atmospheric particles with the frequent and increasing precipitation. The pH values of the 78% samples show neutral pH and neutralization factors (NF) followed a sequence of NF
Ca
˃NF
Mg
˃ NF
NH4
with factors of 0.77, 0.34, and 0.14 indicating Ca
2+
was the most potential species to balance the acidic ions (NO
3
−
, SO
4
2−
) over the study area. Source apportionment study indicates the significant influence of marine actions (long-range transport by monsoonal wind from marine origin, Sea spray, salty soil profile of mangrove) as the major source of ions over Sundarban. The rate of nutrient wet deposition in the form of rainwater was estimated and average monsoonal nitrogen flux was observed 0.87 kg ha
−1
where NO
3
contributes the most (0.60 kg ha
−1
). N and P deposition flux also showed a simultaneous pattern with the seasonal nutrient concentration of surrounding river water, which may be an indication of a possible contribution of atmospheric wet deposition in the spike of monsoonal nutrient concentration in river water.
Gene ontology (GO) is a comprehensive resource for the properties of gene products and their relationships. A similarity measure can be defined between two gene products by utilizing GO, and the ...corresponding similarity score can be treated as a likelihood to interact between them physically. However, GO is being updated regularly by the addition of new terms and removal/merging of obsolete terms. Therefore, the similarity score of interaction may differ from one instance of GO to another. In this paper, we systematically study the impact of the continuous evolution of GO on the performance of similarity measures for the task of scoring confidence of protein–protein interactions (PPIs). We find that the performance of a similarity measure gets affected due to the continuous evolution of GO. We further observe that the degree of robustness of a similarity measure is highly influenced by the particular setting we consider.
Shifts in carbonate dissolution can help understand the exchange of carbon dioxide between the air and water of estuarine systems. Adequate spatial coverage is required to understand these emission ...dynamics. Hence, the distribution of carbonate parameters in three estuaries covering a vast expanse of the Indian Sundarbans is described from total alkalinity (TA), dissolved inorganic carbon (DIC) and pH data collected between 2016 and 2020. The seasonal impacts on inorganic carbon parameters were also studied by comparing pre-monsoon, monsoon, and post-monsoon data compiled from the study period. The estuaries showed the highest TA (up to 2506μmol kg −1) and DIC (up to 2203μmol kg −1) in the pre-monsoon. Both the parameters overall were positively associated with salinity. TA and DIC decreased by 369 and 208μmol kg −1, respectively, in the monsoon compared to pre-monsoon. From the monsoon to the post-monsoon, TA and DIC increased by 121 and 85μmol kg −1, respectively. Both showed strong positive associations with high chlorophyll- aand high dissolved oxygen in the post-monsoon suggesting an important role of primary production in the estuaries in raising the concentrations of inorganic carbon parameters. The carbonate mineral saturation states (ΩCa and ΩAr) followed the same pattern as that of TA and DIC. The pair was always supersaturated although freshwater influence caused the values to drop to close to saturation. While pCO2was mostly supersaturated in the system relative to atmospheric concentration, it became minimal in the post-monsoon corresponding to heightened primary production. Despite high organic carbon recycling in mangroves, the system showed less expression in terms of CO2 emission in a seasonal cycle. Overall, the Indian Sundarbans estuarine system emitted low amounts of CO2 with its estimated water-to-air flux densities varying from 0.40 ± 0.61 (pre-monsoon) to 1.62 ± 1.74 mmol m−2h−1(monsoon).
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