Ecological dichotomies arise in microbial communities due to mixing of deep hydrothermal waters and atmospheric gas in a circumneutral hot spring.

Little is known of how the confluence of subsurface and surface processes influences the assembly and habitability of hydrothermal ecosystems. To address this knowledge gap, the geochemical and microbial composition of a high temperature, circumneutral hot spring in Yellowstone National Park was examined to identify the sources of solutes and their effect on the ecology of microbial inhabitants. Metagenomic analysis showed populations comprising planktonic and sediment communities are archaeal dominated, are dependent on chemical energy (chemosynthetic), share little overlap in their taxonomic composition, and are differentiated by their inferred use of/tolerance to oxygen and mode of carbon metabolism. The planktonic community is dominated by putative aerobic/aerotolerant autotrophs while the taxonomic composition of the sediment community is more evenly distributed and comprised of anaerobic heterotrophs. These observations are interpreted to reflect sourcing of the spring by anoxic, organic carbon-limited subsurface hydrothermal fluids and ingassing of atmospheric oxygen that selects for aerobic/aerotolerant organisms that have autotrophic capabilities in the water column. Autotrophy and consumption of oxygen by the planktonic community may influence the assembly of the anaerobic and heterotrophic sediment community. Support for this inference comes from higher estimated rates of genome replication in planktonic populations than sediment populations, indicating faster growth in planktonic populations. Collectively, these observations provide new insight into how mixing of subsurface waters and atmospheric oxygen create dichotomy in the ecology of hot spring communities and suggest that planktonic and sediment communities may have been less differentiated taxonomically and functionally prior to the rise of oxygen ∼2.4 Gya. IMPORTANCE Understanding the source and availability of energy capable of supporting life in hydrothermal environments is central to predicting the ecology of microbial life on early Earth when volcanic activity was more widespread. Little is known of the substrates supporting microbial life in circumneutral to alkaline springs, despite their relevance to early Earth habitats. Using metagenomic and informatics approaches, water column and sediment habitats in a representative circumneutral hot spring in Yellowstone were shown to be dichotomous, with the former largely hosting aerobic/aerotolerant autotrophs and the latter primarily hosting anaerobic heterotrophs. This dichotomy is attributed to influx of atmospheric oxygen into anoxic deep hydrothermal spring waters. These results indicate that the ecology of microorganisms in circumneutral to alkaline springs sourced by deep hydrothermal fluids was different prior to the rise of atmospheric oxygen ∼ 2.4 Gya, with planktonic and sediment communities likely to be less differentiated than contemporary circumneutral hot springs.

Bacterial community structure of early-stage biofilms is dictated by temporal succession rather than substrate types in the southern coastal seawater of India

Bacterial communities colonized on submerged substrata are recognized as a key factor in the formation of complex biofouling phenomenon in the marine environment. Despite massive maritime activities and a large industrial sector in the nearshore of the Laccadive Sea, studies describing pioneer bacterial colonizers and community succession during the early-stage biofilm are scarce. We investigated the biofilm-forming bacterial community succession on three substrata viz. stainless steel, high-density polyethylene, and titanium over 15 days of immersion in the seawater intake area of a power plant, located in the southern coastal region of India. The bacterial community composition of biofilms and peripheral seawater were analyzed by Illumina MiSeq sequenced 16S rRNA gene amplicons. The obtained metataxonomic results indicated a profound influence of temporal succession over substrate type on the early-stage biofilm-forming microbiota. Bacterial communities showed vivid temporal dynamics that involved variations in abundant bacterial groups. The proportion of dominant phyla viz. Proteobacteria decreased over biofilm succession days, while Bacteroidetes increased, suggesting their role as initial and late colonizers, respectively. A rapid fluctuation in the proportion of two bacterial orders viz. Alteromonadales and Vibrionales were observed throughout the successional stages. LEfSe analysis identified specific bacterial groups at all stages of biofilm development, whereas no substrata type-specific groups were observed. Furthermore, the results of PCoA and UPGMA hierarchical clustering demonstrated that the biofilm-forming community varied considerably from the planktonic community. Phylum Proteobacteria preponderated the biofilm-forming community, while the Bacteroidetes, Cyanobacteria, and Actinobacteria dominated the planktonic community. Overall, our results refute the common assumption that substrate material has a decisive impact on biofilm formation; rather, it portrayed that the temporal succession overshadowed the influence of the substrate material. Our findings provide a scientific understanding of the factors shaping initial biofilm development in the marine environment and will help in designing efficient site-specific anti-biofouling strategies.

Detection of sulfate-reducing bacteria as an indicator for successful mitigation of sulfide production

Sulfate-reducing bacteria (SRB) are one of the main sources of biogenic H 2 S generation in oil reservoirs. Excess H 2 S production in these systems leads to oil biosouring, which causes operational risks, health hazards and can increase the cost of refining crude oil. Nitrate salts are often added to the system to suppress sulfidogenesis. Because SRB populations can persist in biofilms even after nitrate treatment, identifying shifts in the sessile community is crucial for successful mitigation. However, sampling the sessile community is hampered by its inaccessibility. Here we use the results of a long-term (148 days) ex situ experiment to identify particular sessile community members from observations of the sample waste stream. Microbial community structure was determined for 731 samples across twenty bioreactors using 16S rRNA gene sequencing. By associating microbial community structure with specific steps in the mitigation process, we could distinguish between taxa associated with H 2 S production and mitigation. After initiation of nitrate treatment, certain SRB populations increased in the planktonic community during critical time points, indicating the dissociation of SRBs from the biofilm. Predicted relative abundances of the dissimilatory sulfate reduction pathway also increased during the critical time points. Here, by analyzing the planktonic community structure, we describe a general method that uses high-throughput amplicon sequencing, metabolic inferences, and cell abundance data to identify successful biofilm mitigation. We anticipate that our approach is also applicable to other systems where biofilms must be mitigated but cannot be easily sampled. Importance Microbial biofilms are commonly present in many industrial processes and can negatively impact performance and safety. Within the oil industry, subterranean biofilms cause biosouring with implications for oil quality, cost, occupational health, and the environment. Because these biofilms cannot be directly sampled, methods are needed to indirectly assess the success of mitigation measures. This study demonstrates how the planktonic microbial community can be used to assess the dissociation of SRB-containing biofilms. We found that an increase in the abundance of a specific SRB population in the effluent after nitrate treatment can be used as a potential indicator for the successful mitigation of biofilm-forming SRBs. Moreover, a method for determining critical time points for detecting potential indicators is suggested. This study expands our knowledge in improving mitigation strategies for biosouring and could have broader implications in other systems where biofilms lead to adverse consequences.

An in vitro model for the cultivation of polymicrobial biofilms under continuous-flow conditions

The airways of people with cystic fibrosis (CF) are often chronically colonised with a diverse array of bacterial and fungal species. However, little is known about the relative partitioning of species between the planktonic and biofilm modes of growth in the airways. Existing in vivo and in vitro models of CF airway infection are ill-suited for the long-term recapitulation of mixed microbial communities. Here we describe a simple, in vitro continuous-flow model for the cultivation of polymicrobial biofilms and planktonic cultures on different substrata. Our data provide evidence for inter-species antagonism and synergism in biofilm ecology. We further show that the type of substratum on which the biofilms grow has a profound influence on their species composition. This happens without any major alteration in the composition of the surrounding steady-state planktonic community. Our experimentally-tractable model enables the systematic study of planktonic and biofilm communities under conditions that are nutritionally reminiscent of the CF airway microenvironment, something not possible using any existing in vivo models of CF airway infection.

Zooplankton trophic dynamics drive carbon export efficiency

The flux of detrital particles produced by plankton is an important component of the biological carbon pump. We investigate how food web structure and organisms’ size regulate particulate carbon export efficiency (the fraction of primary production that is exported via detrital particles at a given depth). We use the Nutrient-Unicellular-Multicellular (NUM) mechanistic size-spectrum model of the planktonic community (unicellular pro-tists and copepods), embedded within a 3D model representation of the global ocean circulation. The ecosystem model generates emergent food webs and size distributions of all organisms and detrital particles. Model outputs are compared to field data. We find that strong predation by copepods increases export efficiency, while protist predation reduces it. We find no clear relation between primary production and export efficiency. Temperature indirectly drives carbon export efficiency by affecting the biomass of copepods. High temperatures, combined with nutrient limitation, result in low growth efficiency, smaller trophic transfer to higher trophic levels, and decreased carbon export efficiency. Even though copepods consume a large fraction of the detritus produced, they do not markedly attenuate the particle flux. Our simulations illustrate the complex relation between the planktonic food web and export efficiency, and highlights the central role of zooplankton and their size structure.Plain Language SummaryPlankton are small organisms that live in the ocean. Plankton remove CO2 from the atmosphere by doing photosynthesis and sinking to the deep ocean, where the CO2 is sequestered. Photosynthesis can be measured by satellites, and therefore, knowing the fraction of photosynthesis that sinks to the deep ocean could allow making more accurate predictions of the concentration of CO2 in the atmosphere. This fraction of photosynthesis that is exported is termed “carbon export efficiency”. However, the drivers that define this carbon export efficiency are not well understood. To explore these drivers, we used computer simulations that include many planktonic organisms in a 3D model of the oceans. The model generates a detailed representation of the body sizes of plankton and of particle sizes, which is one of the main features defining sinking rates of particles in nature. We find that export efficiency is high when large zooplankton consume large amounts of prey. Temperature decreases export efficiency by reducing how efficient large plankton grow. Finally, we do not find a clear relation between photosynthesis and export efficiency, which has been much discussed in the literature. This provides mechanistic explanations to previous field observations and generates new hypotheses to be tested.Key Points:We used a 3D size-spectrum model of the planktonic community to understand the drivers of particulate carbon export efficiencyWe find that high temperature decreases growth efficiency, trophic transfer efficiency and associated carbon export efficiency.Systems that are top-down controlled by zooplankton can have high export efficiencies depending on the size of the dominant zooplankton.

Using sedaDNA to reconstruct planktonic communities across 385’000 years old marine sedimentary core from a tropical sea.

<p>Sedimentary ancient DNA (sedaDNA) is becoming a paleo-proxy of choice for many marine environments. However, there are few studies from tropical sites and even fewer from tropical marine sediments exposed to factors damaging the DNA such as elevated sea surface water temperature or UV radiation. Here, we report successful extraction of DNA from a marine sedimentary core retrieved from the Bismarck Sea, off New Papua Guinea, where the mean annual temperature is about 29°C. The core MD05-2920 covers the last 385 000 years. We analyzed samples from 20 layers, where the isotopic measures of δ<sup>18</sup>O isotopic composition of benthic foraminifera show significant palaeoceanographic changes from glacial to interglacial periods. We apply a metabarcoding approach using specific 18S primers for planktonic foraminifera, diatoms, and radiolarians. Even if the amount of DNA declines throughout the core, the patterns of successional changes in species communities of these three taxonomic groups are well archived. Our study shows that it is possible to reconstruct the planktonic community even from very old sedaDNA samples from a tropical marine sedimentary core.</p>

PLANKTONIC COMMUNITY IN WATERBODIES OF THE KHARANORSKAYA SDPP: CURRENT STATE AND DINAMICS

This paper presents the results of studies of phyto- and zoop-lankton communities in reser-voirs of the Kharanorskaya SDPP cooling system (cooling pond, water supply and drai-nage channels), conducted in April, July and October of 2019. Long-term changes in the diversity and structure of planktonic associations during 1995–2019 are analyzed. A total of 141 taxa of algae ranked below the genus level and 52 taxa of invertebrates are identified in plankton. The phytoplankton total abundance and total biomass changed from 20 to 742×103 cells/l and from 65 to 711 mg/m3; zooplankton, from 7 to 212×103 ind./m3 and from 0.01 to 2.7 g/m3. The greatest abundance of algae was observed in summer and autumn, invertabrates – in spring and summer. Long-term observations of planktonic biocenoses show an increase in the species richness of diatoms and rotifers and a decrease in green algal and chrysophyts. Also there is a tendency towards a decrease in the phyto- and zooplankton total abundance as the abundance of cyanophytes, green algal, rotifers and cladocerans increases.