Newly identified HMO-2011-type phages reveal genomic diversity and biogeographic distributions of this marine viral group

Viruses play critical roles in influencing biogeochemical cycles and adjusting host mortality, population structure, physiology, and evolution in the ocean. Marine viral communities are composed of numerous genetically distinct subfamily/genus-level viral groups. Among currently identified viral groups, the HMO-2011-type group is known to be dominant and broadly distributed. However, only four HMO-2011-type cultivated representatives that infect marine SAR116 and Roseobacter strains have been reported to date, and the genetic diversity, potential hosts, and ecology of this group remain poorly elucidated. Here, we present the genomes of seven HMO-2011-type phages that were isolated using four Roseobacter strains and one SAR11 strain, as well as additional 207 HMO-2011-type metagenomic viral genomes (MVGs) identified from various marine viromes. Phylogenomic and shared-gene analyses revealed that the HMO-2011-type group is a subfamily-level group comprising at least 10 discernible genus-level subgroups. Moreover, >2000 HMO-2011-type DNA polymerase sequences were identified, and the DNA polymerase phylogeny also revealed that the HMO-2011-type group contains diverse subgroups and is globally distributed. Metagenomic read-mapping results further showed that most HMO-2011-type phages are prevalent in global oceans and display distinct geographic distributions, with the distribution of most HMO-2011-type phages being associated with temperature. Lastly, we found that members in subgroup IX, represented by pelagiphage HTVC033P, were among the most abundant HMO-2011-type phages, which implies that SAR11 bacteria are crucial hosts for this viral group. In summary, our findings substantially expand current knowledge regarding the phylogenetic diversity, evolution, and distribution of HMO-2011-type phages, highlighting HMO-2011-type phages as major ecological agents that can infect certain key bacterial groups.

Sound Scattering Layers Within and Beyond the Seychelles-Chagos Thermocline Ridge in the Southwest Indian Ocean

In global oceans, ubiquitous and persistent sound scattering layers (SL) are frequently detected with echosounders. The southwest Indian Ocean has a unique feature, a region of significant upwelling known as the Seychelles-Chagos Thermocline Ridge (SCTR), which affects sea surface temperature and marine ecosystems. Despite their importance, sound SL within and beyond the SCTR are poorly understood. This study aimed to compare the characteristics of the sound SL within and beyond the SCTR in connection with environmental properties, and dominant zooplankton. To this end, the region north of the 12°S latitude in the survey area was defined as SCTR, and the region south of 12°S was defined as non-SCTR. The results indicated contrasting oceanographic properties based on the depth layers between SCTR and non-SCTR regions. Distribution dynamics of the sound SL differed between the two regions. In particular, the diel vertical migration pattern, acoustic scattering values, metrics, and positional properties of acoustic scatterers showed two distinct features. In addition, the density of zooplankton sampled was higher in SCTR than in the non-SCTR region. This is the first study to present bioacoustic and hydrographic water properties within and beyond the SCTR in the southwest Indian Ocean.

The Impact of COVID-19 Lockdowns on Satellite-Observed Aerosol Optical Thickness over the Surrounding Coastal Oceanic Areas of Megacities in the Coastal Zone

Nearly 40 years of aerosol optical thickness (AOT) climate data record (CDR) derived from NOAA operational satellite Advanced Very High Resolution Radiometer (AVHRR) observation over the global oceans is used to study the AOT changes due to the COVID-19 lockdown over the surrounding coastal oceanic areas of 18 megacities in the coast zone (MCCZ). The AOT difference between the annual mean AOT values of 2020 with COVID-19 lockdown and 2019 without the lockdown along with the 2020 AOT annual anomaly are used to effectively identify the AOT changes that are a result of the lockdown. We found that for most of the 18 MCCZ, the COVID-19 lockdowns implemented to contain the spread of the coronavirus resulted in a decrease between 1% and 30% in AOT due to reduced anthropogenic emissions associated with the lockdowns. However, the AOT long-term trend and other aerosol interannual variations due to favorable or unfavorable meteorological conditions may mask AOT changes due to the lockdown effect in some MCCZ. Different seasonal variations of aerosol amount in 2020 relative to 2019 due to other natural aerosol emission sources not influenced by the lockdown, such as dust storms and natural biomass burning and smoke, may also conceal a limited reduction in the annual mean AOT due to the lockdown in MCCZ with relatively loose lockdown. This study indicates that the use of long-term satellite observation is helpful for studying and monitoring the aerosol changes due to the emission reduction associated with the COVID-19 lockdown in the surrounding coastal oceanic areas of MCCZ, which will benefit the future development of the mitigation strategy for air pollution and emissions in megacities.

Report of Epibiont Diatom P. pacificum on the Cyclopoid Copepod D. affinis from the Southwestern Shelf Waters of India (Eastern Arabian Sea)

Pseudohimantidium pacificum, an epizoic diatom has been reported from different parts of the global oceans, however, has not been reported from the shelf waters of India. This symbiotic association of P. pacificum with a specific copepod species (Ditrichocorycaeus affinis) was repeatedly noticed from the shelf waters of the Arabian Sea during the winter monsoon from three locations in the South East Arabian Sea. Our study suggests towards host specificity of P. pacificum and additionally reveals their preference towards male hosts which is consistent with the earlier reports from other regions. Most importantly, this report extends the range of geographic distribution of the epibiont and this is the third report on this epibiont from the Indian Ocean region. It also suggests that epibiosis in marine zooplankton is much frequent phenomenon that has the potential to play an important role in the marine zooplankton population dynamics.

D-alanine metabolism via D-Ala aminotransferase by marine Gammaproteobacteria , Pseudoalteromonas sp. CF6-2

As the most abundant D-amino acid (DAA) in the ocean, D-alanine (D-Ala) is a key component of peptidoglycan in bacterial cell wall. However, the underlying mechanisms of bacterial metabolization of D-Ala through microbial food web remain largely unknown. In this study, the metabolism of D-Ala by marine bacterium Pseudoalteromonas sp. CF6-2 was investigated. Based on genomic, transcriptional and biochemical analyses combined with gene knockout, D-Ala aminotransferase was found to be indispensable for the catabolism of D-Ala in strain CF6-2. Investigation on other marine bacteria also showed that D-Ala aminotransferase gene is a reliable indicator for their ability to utilize D-Ala. Bioinformatic investigation revealed that D-Ala aminotransferase sequences are prevalent in genomes of marine bacteria and metagenomes, especially in seawater samples, and Gammaproteobacteria represents the predominant group containing D-Ala aminotransferase. Thus, Gammaproteobacteria is likely the dominant group to utilize D-Ala via D-Ala aminotransferase to drive the recycling and mineralization of D-Ala in the ocean. IMPORTANCE As the most abundant D-amino acid in the ocean, D-Ala is a component of marine DON (Dissolved organic nitrogen) pool. However, the underlying mechanism of bacterial metabolization of D-Ala to drive the recycling and mineralization of D-Ala in the ocean is still largely unknown. The results in this study showed that D-Ala aminotransferase is specific and indispensable for D-Ala catabolism in marine bacteria, and that marine bacteria containing D-Ala aminotransferase genes are predominantly Gammaproteobacteria widely distributed in global oceans. This study reveals marine D-Ala utilizing bacteria and the mechanism of their metabolization of D-Ala. The results shed light on the mechanisms of recycling and mineralization of D-Ala driven by bacteria in the ocean, which are helpful in understanding oceanic microbial-mediated nitrogen cycle.