Manuscript Topics

Single celled phytoplankton and photosynthetic cyanobacteria constitute the base of the food web in marine environments. Primary consumption by zooplankton as well as viral termination of algal and bacterial blooms releases dissolved organic matter, which flows back to the higher trophic levels in the form of newly produced bacterial biomass (i.e., the microbial loop). Subsequently, zooplankton are an important food source for secondary consumers including many fish species. Sustaining a balanced microbial loop is thus essential to secure the overall health and functioning of entire marine ecosystems. In addition, many nations depend on the healthy functioning of coastal aquatic ecosystems as they provide an economically important food stable for human consumption. Changes in salinity, oxygen content, temperature, and nutrient availability can affect the population dynamics and overall functioning of the microbial loop. Human activities such as deforestation and increased land use for agricultural activities causes increased terrestrial runoff of nutrients into aquatic environments. Whereas several thousands of years ago humans already started to change the coastal landscape in many regions of the world, long-term records of microbial ecosystem changes caused by anthropogenic activities are limited and/or are restricted to documenting the minority of taxa that left behind diagnostic microscopic features and/or chemical fossils (lipid biomarkers) in sedimentary records. In addition, extracting and sequencing genetic signatures of past plankton preserved in aquatic sedimentary archives (i.e., sediment ancient DNA; sed aDNA) is rapidly gaining popularity. Paired with paleoenvironmental proxy data, analysis of ancient plankton DNA using molecular tools has shown to be an extremely promising approach in elucidating whole ecosystem responses (including members of the microbial loop that lack a fossil record) to natural Quaternary climate variability vs. more recent anthropogenic perturbations plus the role microbial communities have played in past biogeochemical cycling processes. Using sed aDNA approaches it has also become possible to generate long-term records of viral termination of algal blooms as well as parasitic vs. mutualistic microbial interactions (see Armbrecht et al., 2019 and Capo et al., 2021 for a review). Marine coastal sed aDNA records are still severely understudied especially from the tropics and there are several challenges to overcome before it is possible to take full advantage of the rapidly evolving field of sedimentary paleogenomics. For example, the need to improve our ability to distinguish between active indigenous sedimentary microbial communities that are shaped by in situ environmental conditions vs. dormant or dead counterparts that were seeded from the ancient water column and that may provide long-term genomic records of ecosystem responses to paleo environmental perturbations. The need to develop approaches, such as hybridization capture techniques (Armbrecht et al., 2021), to avoid the capturing and sequencing of the vast majority of genetic markers from modern microbial communities, and yet selective enrich trace levels of preserved marker genes to drastically lower the detection limit of past microbial communities of interest.    
These examples serve as a guideline only. For this special issue we welcome all contributions that involve the study of paleomicrobiomes preserved in sedimentary records from coastal marine environments as well as from marine influenced basins and terrestrial saline lakes.

Potential topics include, but not limited to  
• Paleomicrobiology  
• Ancient sedimentary DNA  
• Biogeochemical cycling  
• Paleoclimate  
• Anthropocene  
• Genome evolution  
• Molecular paleoecology

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