Cellular interactions: lessons from the nitrogen‐fixing cyanobacteria

Marine nitrogen‐fixing cyanobacteria play a central role in the open‐ocean microbial community by providing fixed nitrogen (N) to the ocean from atmospheric dinitrogen (N₂) gas. Once thought to be dominated by one genus of cyanobacteria, Trichodesmium, it is now clear that marine N₂‐fixing cyanobacteria in the open ocean are more diverse, include several previously unknown symbionts, and are geographically more widespread than expected. The next challenge is to understand the ecological implications of this genetic and phenotypic diversity for global oceanic N cycling. One intriguing aspect of the cyanobacterial N₂ fixers ecology is the range of cellular interactions they engage in, either with cells of their own species or with photosynthetic protists. From organelle‐like integration with the host cell to a free‐living existence, N₂‐fixing cyanobacteria represent the range of types of interactions that occur among microbes in the open ocean. Here, we review what is known about the cellular interactions carried out by marine N₂‐fixing cyanobacteria and where future work can help. Discoveries related to the functional roles of these specialized cells in food webs and the microbial community will improve how we interpret their distribution and abundance patterns and contributions to global N and carbon (C) cycles.     

Shifts in microbial community structure and function in light‐ and dark‐grown biofilms driven by warming

Biofilms are dynamic players in biogeochemical cycling in running waters and are subjected to environmental stressors like those provoked by climate change. We investigated whether a 2°C increase in flowing water would affect prokaryotic community composition and heterotrophic metabolic activities of biofilms grown under light or dark conditions. Neither light nor temperature treatments were relevant for selecting a specific bacterial community at initial phases (7‐day‐old biofilms), but both variables affected the composition and function of mature biofilms (28‐day‐old). In dark‐grown biofilms, changes in the prokaryotic community composition due to warming were mainly related to rotifer grazing, but no significant changes were observed in functional fingerprints. In light‐grown biofilms, warming also affected protozoan densities, but its effect on prokaryotic density and composition was less evident. In contrast, heterotrophic metabolic activities in light‐grown biofilms under warming showed a decrease in the functional diversity towards a specialized use of several carbohydrates. Results suggest that prokaryotes are functionally redundant in dark biofilms but functionally plastic in light biofilms. The more complex and self‐serving light‐grown biofilm determines a more buffered response to temperature than dark‐grown biofilms. Despite the moderate increase in temperature of only 2°C, warming conditions drive significant changes in freshwater biofilms, which responded by finely tuning a complex network of interactions among microbial populations within the biofilm matrix.     

Deep‐water anoxygenic photosythesis in a ferruginous chemocline

Ferruginous Lake Matano, Indonesia hosts one of the deepest anoxygenic photosynthetic communities on Earth. This community is dominated by low‐light adapted, BChl e‐synthesizing green sulfur bacteria (GSB), which comprise ~25% of the microbial community immediately below the oxic‐anoxic boundary (OAB; 115‐120 m in 2010). The size of this community is dependent on the mixing regime within the lake and the depth of the OAB—at ~117 m, the GSB live near their low‐light limit. Slow growth and C‐fixation rates suggest that the Lake Matano GSB can be supported by sulfide even though it only accumulates to scarcely detectable (low μm to nm ) concentrations. A model laboratory strain (Chlorobaculum tepidum) is indeed able to access HS^? for oxidation at nm concentrations. Furthermore, the GSB in Lake Matano possess a full complement of S‐oxidizing genes. Together, this physiological and genetic information suggests that deep‐water GSB can be supported by a S‐cycle, even under ferruginous conditions. The constraints we place on the metabolic capacity and physiology of GSB have important geobiological implications. Biomarkers diagnostic of GSB would be a good proxy for anoxic conditions but could not discriminate between euxinic and ferruginous states, and though GSB biomarkers could indicate a substantial GSB community, such a community may exist with very little metabolic activity. The light requirements of GSB indicate that at light levels comparable to those in the OAB of Lake Matano or the Black Sea, GSB would have contributed little to global ocean primary production, nutrient cycling, and banded iron formation (BIF) deposition in the Precambrian. Before the proliferation of oxygenic photosynthesis, shallower OABs and lower light absorption in the ocean's surface waters would have permitted greater light availability to GSB, potentially leading to a greater role for GSB in global biogeochemical cycles.     

Metabolic reprogramming by viruses in the sunlit and dark ocean

Background

Marine ecosystem function is largely determined by matter and energy transformations mediated by microbial community interaction networks. Viral infection modulates network properties through mortality, gene transfer and metabolic reprogramming.

Results

Here we explore the nature and extent of viral metabolic reprogramming throughout the Pacific Ocean depth continuum. We describe 35 marine viral gene families with potential to reprogram metabolic flux through central metabolic pathways recovered from Pacific Ocean waters. Four of these families have been previously reported but 31 are novel. These known and new carbon pathway auxiliary metabolic genes were recovered from a total of 22 viral metagenomes in which viral auxiliary metabolic genes were differentiated from low-level cellular DNA inputs based on small subunit ribosomal RNA gene content, taxonomy, fragment recruitment and genomic context information. Auxiliary metabolic gene distribution patterns reveal that marine viruses target overlapping, but relatively distinct pathways in sunlit and dark ocean waters to redirect host carbon flux towards energy production and viral genome replication under low nutrient, niche-differentiated conditions throughout the depth continuum.

Conclusions

Given half of ocean microbes are infected by viruses at any given time, these findings of broad viral metabolic reprogramming suggest the need for renewed consideration of viruses in global ocean carbon models.     

The novel use of pop‐off satellite tags (PSATs) to investigate the migratory behaviour of European sea bass Dicentrarchus labrax

A total of 12 adult European sea bass Dicentrarchus labrax were tagged with pop‐off satellite archival tags (PSAT) in Irish coastal waters and in offshore waters in the north‐east Celtic Sea between 2015 and 2016. Archived data were successfully recovered from five of the 12 tags deployed, three from fish released in inshore Irish waters and two from fish released offshore in the eastern Celtic Sea. All three fish tagged in inshore waters were found to undertake migrations into the open ocean coinciding with the spawning period. These fish also exhibited fidelity to inshore sites post‐migration, returning to the same general location (within c. 73 km, which is roughly the predicted mean accuracy of the method) of their original release site. Although the number of tracks obtained here was limited, some degree of aggregation between inshore and offshore tagged fish in the eastern Celtic Sea was noted during the expected spawning period suggesting PSATs can provide new information on specific spawning locations of European sea bass.     

Nitrate Uptake by Reef Corals

In specimens of the hermatypic coral species Fungia scutaria and Montipora verrucosa and in the alga Ulva lactuca, nitrate uptake was measured in light and dark with a flow-through apparatus. The nitrate uptake was measurable in high-nitrate bay water of Kaneohe Bay and also in low-nitrate open ocean water. Nitrate consumption rates by the corals and the alga did not differ from light to dark. Neither the coral nor the alga showed measurable immediate nitrate uptake in open ocean water of low nitrate concentration when they had been held previously in the high-nitrate bay water. In low-nitrate open ocean water the uptake per unit time increases when the flow of the water increases. The uptake of nitrate by reef corals even from low concentrations indicates nonspecific nutrient sources for reef corals.     

Diurnal fluctuations in chloroplast GSH redox state regulate susceptibility to oxidative stress and cell fate in a bloom‐forming diatom

Diatoms are one of the key phytoplankton groups in the ocean, forming vast oceanic blooms and playing a significant part in global primary production. To shed light on the role of redox metabolism in diatom's acclimation to light–dark transition and its interplay with cell fate regulation, we generated transgenic lines of the diatom Thalassiosira pseudonana that express the redox‐sensitive green fluorescent protein targeted to various subcellular organelles. We detected organelle‐specific redox patterns in response to oxidative stress, indicating compartmentalized antioxidant capacities. Monitoring the GSH redox potential (E_GSH) in the chloroplast over diurnal cycles revealed distinct rhythmic patterns. Intriguingly, in the dark, cells exhibited reduced basal chloroplast E_GSH but higher sensitivity to oxidative stress than cells in the light. This dark‐dependent sensitivity to oxidative stress was a result of a depleted pool of reduced glutathione which accumulated during the light period. Interestingly, reduction in the chloroplast E_GSH was observed in the light phase prior to the transition to darkness, suggesting an anticipatory phase. Rapid chloroplast E_GSH re‐oxidation was observed upon re‐illumination, signifying an induction of an oxidative signaling during transition to light that may regulate downstream metabolic processes. Since light–dark transitions can dictate metabolic capabilities and susceptibility to a range of environmental stress conditions, deepening our understanding of the molecular components mediating the light‐dependent redox signals may provide novel insights into cell fate regulation and its impact on oceanic bloom successions.     

Zooplankton community and hydrographical properties of the Neretva Channel (eastern Adriatic Sea)

Temporal and spatial variability of micro and mesozooplankton was studied in 1998 and 1999 at four stations in the Neretva Channel area influenced by the Neretva river and the open waters of the south Adriatic Sea. The area is orthophosphate limited, but an excessive accumulation of land derived nitrogen is prevented by phytoplankton uptake and the general circulation pattern. Microzooplankton was dominated by ciliates, with average abundances comparable to other Adriatic channel areas (122–543 ind. l⁻¹). Non-loricate ciliates (NLC) generally peaked in the warmer periods, but a winter increase was evident towards the inner part of the channel. Tintinnid abundances generally increased in autumn. A significant relationship with temperature was not recorded for either protozoan group. An inverse relationship between NLC and salinity might be indirectly caused by their preference for the food abundant surface layer. Mesozooplankton was dominated by copepods, with distinct summer maxima throughout the area and pronounced winter maxima of >10,000 ind. m⁻³ at the inner stations. The community was predominantly neritic but the open sea waters were important in structuring the mesozooplankton assemblage at all stations during the autumn–winter period. Although temperature regulated the seasonal dynamics of most metazoans and the species succession in the copepod community, small omnivorous copepods (Oncaea media complex, Oithona nana and Euterpina acutifrons) dominated regardless of the season. A trophic link between copepods and ciliates was evident in winter during low phytoplankton biomass.     

Archaeal biogeography and interactions with microbial community across complex subtropical coastal waters

Marine Archaea are crucial in biogeochemical cycles, but their horizontal spatial variability, assembly processes, and microbial associations across complex coastal waters still lack characterizations at high coverage. Using a dense sampling strategy, we investigated horizontal variability in total archaeal, Thaumarchaeota Marine Group (MG) I, and Euryarchaeota MGII communities and associations of MGI/MGII with other microbes in surface waters with contrasting environmental characteristics across ~200 km by 16S rRNA gene amplicon sequencing. Total archaeal communities were extremely dominated by MGI and/or MGII (98.9% in average relative abundance). Niche partitioning between MGI and MGII or within each group was found across multiple environmental gradients. “Selection” was more important than “dispersal limitation” in governing biogeographic patterns of total archaeal, MGI, and MGII communities, and basic abiotic parameters (such as salinity) and inorganic/organic resources as a whole could be the main driver of “selection”. While “homogenizing dispersal” also considerably governed their biogeography. MGI‐Nitrospira assemblages were speculatively responsible for complete nitrification. MGI taxa commonly had negative correlations with members of Synechococcus but positive correlations with members of eukaryotic phytoplankton, suggesting that competition or synergy between MGI and phytoplankton depends on specific MGI‐phytoplankton assemblages. MGII taxa showed common associations with presumed (photo)heterotrophs including members of SAR11, SAR86, SAR406, and Candidatus Actinomarina. This study sheds light on ecological processes and drivers shaping archaeal biogeography and many strong MGI/MGII‐bacterial associations across complex subtropical coastal waters. Future efforts should be made on seasonality of archaeal biogeography and biological, environmental, or ecological mechanisms underlying these statistical microbial associations.     

Microbial community composition and hydrochemistry of underexplored geothermal waters in Croatia

In Croatia, a variety of geothermal springs with a wide temperature range and varied hydrochemical conditions exist, and they may harbor different niches for the distribution of microbial communities. In this study, 19 different sites, mainly located in central and eastern Croatia, were selected for primary characterization of spring hydrochemistry and microbial community composition. Using 16S rRNA gene amplicon sequencing, it was found that the bacterial communities that dominated most geothermal waters were related to Proteobacteria and Campylobacteria, while most archaeal sequences were related to Crenarchaeota. At the genus level, the prokaryotic community was highly site-specific and was often dominated by a single genus, including sites dominated by Hydrogenophilus, Sulfuricurvum, Sulfurovum, Thiofaba and Nitrospira, while the most abundant archaeal genera were affiliated to the ammonia-oxidizing archaea, Candidatus Nitrosotenuis and Candidatus Nitrososphaera. Whereas the microbial communities were overall highly location-specific, temperature, pH, ammonia, nitrate, total nitrogen, sulfate and hydrogen sulfide, as well as dissolved organic and inorganic carbon, were the abiotic factors that significantly affected microbial community composition. Furthermore, an aquifer-type effect was observed in the community composition, but there was no pronounced seasonal variability for geothermal spring communities (i.e. the community structure was mainly stable during the three seasons sampled). These results surprisingly pointed to stable and geographically unique microbial communities that were adapted to different geothermal water environments throughout Croatia. Knowing which microbial communities are present in these extreme habitats is essential for future research. They will allow us to explore further the microbial metabolisms prevailing at these geothermal sites that have high potential for biotechnological uses, as well as the establishment of the links between microbial community structure and the physicochemical environment of geothermal waters.     

Estuary–ocean connectivity: fast physics,slow biology

Estuaries are connected to both land and ocean so their physical, chemical, and biological dynamics are influenced by climate patterns over watersheds and ocean basins. We explored climate‐driven oceanic variability as a source of estuarine variability by comparing monthly time series of temperature and chlorophyll‐a inside San Francisco Bay with those in adjacent shelf waters of the California Current System (CCS) that are strongly responsive to wind‐driven upwelling. Monthly temperature fluctuations inside and outside the Bay were synchronous, but their correlations weakened with distance from the ocean. These results illustrate how variability of coastal water temperature (and associated properties such as nitrate and oxygen) propagates into estuaries through fast water exchanges that dissipate along the estuary. Unexpectedly, there was no correlation between monthly chlorophyll‐a variability inside and outside the Bay. However, at the annual scale Bay chlorophyll‐a was significantly correlated with the Spring Transition Index (STI) that sets biological production supporting fish recruitment in the CCS. Wind forcing of the CCS shifted in the late 1990s when the STI advanced 40 days. This shift was followed, with lags of 1–3 years, by 3‐ to 19‐fold increased abundances of five ocean‐produced demersal fish and crustaceans and 2.5‐fold increase of summer chlorophyll‐a in the Bay. These changes reflect a slow biological process of estuary–ocean connectivity operating through the immigration of fish and crustaceans that prey on bivalves, reduce their grazing pressure, and allow phytoplankton biomass to build. We identified clear signals of climate‐mediated oceanic variability in this estuary and discovered that the response patterns vary with the process of connectivity and the timescale of ocean variability. This result has important implications for managing nutrient inputs to estuaries connected to upwelling systems, and for assessing their responses to changing patterns of upwelling timing and intensity as the planet continues to warm.     

New insights into relationships between active and dormant organisms,phylogenetic diversity and ecosystem productivity

Marine microbes make up a key part of ocean food webs and drive ocean chemistry through a range of metabolic processes. A fundamental question in ecology is whether the diversity of organisms in a community shapes the ecological functions of that community. While there is substantial evidence to support a positive link between diversity and ecological productivity for macro‐organisms in terrestrial environments, this relationship has not previously been verified for marine microbial communities. One factor complicating the understanding of this relationship is that many marine microbes are dormant and are easily dispersed by ocean currents, making it difficult to ensure that the organisms found in a given environmental sample accurately reflect processes occurring in that environment. Another complication is that, due to microbes great range of genotypic and phenotypic variability, communities with distantly related species may have greater range of metabolic functions than communities have the same richness and evenness, but in which the species present are more closely related to each other. In this issue of Molecular Ecology, Galand et al. (2015) provide compelling evidence that the most metabolically active communities are those in which the nondormant portion of the microbial community has the highest phylogenetic diversity. They also illustrate that focusing on the active portion of the community allows for detection of temporal patterns in community structure that would not be otherwise evident. The authors’ point out that the presence of many dormant organisms that do not contribute to ecosystem functioning is a feature that makes microbial ecosystems fundamentally different from macro‐ecosystems and that this difference needs to be accounted for in microbial ecology theory.     

Estimation of oxygen evolution by marine phytoplankton from measurement of the efficiency of Photosystem II electron flow

The relation between photosynthetic oxygen evolution and Photosystem II electron transport was investigated for the marine algae t Phaeodactylum tricornutum, Dunaliella tertiolecta, Tetraselmis sp., t Isochrysis sp. and t Rhodomonas sp.. The rate of Photosystem II electron transport was estimated from the incident photon flux density and the quantum efficiency of Photosystem II electron transport as determined by chlorophyll fluorescence. The relation between the estimated rate of Photosystem II electron transport and the rate of oxygen evolution was investigated by varying the ambient light intensity. At limiting light intensities a linear relation was found in all species. At intensities approaching light saturation, the relation was found to deviate from linearity. The slope of the line in the light-limited range is species dependent and related to differences in absorption cross-section of Photosystem II. The observed non-linearity at high irradiances is not caused by photorespiration but probably by a Mehler-type of oxygen reduction. The relationship could be modelled by including a redox-state dependent oxygen uptake. In the diatom t Phaeodactylum tricornutum, the photochemical efficiency of dark adapted open Photosystem II centers was found to be temperature-dependent with an optimum near 10°C.     

Inter‐α‐inhibitor deficiency in the mouse is associated with alterations in anxiety‐like behavior,exploration and social approach

In recent years, several genome‐wide association studies have identified candidate regions for genetic susceptibility in major mood disorders. Most notable are regions in a locus in chromosome 3p21, encompassing the genes NEK4‐ITIH1‐ITIH3‐ITIH4. Three of these genes represent heavy chains of the composite protein inter‐α‐inhibitor (IαI). In order to further establish associations of these genes with mood disorders, we evaluated behavioral phenotypes in mice deficient in either Ambp/bikunin, which is necessary for functional ITIH1 and ITIH3 complexes, or in Itih4, the gene encoding the heavy chain Itih4. We found that loss of Itih4 had no effect on the behaviors tested, but loss of Ambp/bikunin led to increased anxiety‐like behavior in the light/dark and open field tests and reduced exploratory activity in the elevated plus maze, light/dark preference and open field tests. Ambp/bikunin knockout mice also exhibited a sex‐dependent exaggeration of acoustic startle responses, alterations in social approach during a three‐chamber choice test, and an elevated fear conditioning response. These results provide experimental support for the role of ITIH1/ITIH3 in the development of mood disorders.     

DarkDivNet – A global research collaboration to explore the dark diversity of plant communities

DarkDivNet is a global research collaboration which explores dark diversity — the set of species that are absent from a site despite being suitable under the site conditions and present in the region. Participants of the network survey vascular plant diversity both at local (10  m × 10 m) and regional scales (radius 10 km) using a standardized approach. They also measure simple plant traits and collect soil samples. Observed and dark diversity together form the site‐specific species pool, and the ratio of observed diversity and dark diversity describes community completeness. We shall explore how observed and dark diversity, site‐specific species pool and community completeness vary across natural and anthropogenic gradients. We link plant diversity measures to the information obtained from environmental DNA: soil biota and plant taxa that occurred at the site before. We will refine existing dark diversity methods and use large vegetation databases to infer species habitat suitability. We expand the dark diversity concept from a purely taxonomy‐based approach to include the functional and phylogenetic aspects of diversity. DarkDivNet currently includes 161 planned sampling areas globally, but new participants are welcome. The main vegetation sampling period is scheduled until September 2020, with the first research papers being produced after that.     

Microbes mediating the sulfur cycle in the Atlantic Ocean and their link to chemolithoautotrophy

Only about 10%–30% of the organic matter produced in the epipelagic layers reaches the dark ocean. Under these limiting conditions, reduced inorganic substrates might be used as an energy source to fuel prokaryotic chemoautotrophic and/or mixotrophic activity. The aprA gene encodes the alpha subunit of the adenosine-5′-phosphosulfate (APS) reductase, present in sulfate-reducing (SRP) and sulfur-oxidizing prokaryotes (SOP). The sulfur-oxidizing pathway can be coupled to inorganic carbon fixation via the Calvin–Benson–Bassham cycle. The abundances of aprA and cbbM, encoding RuBisCO form II (the key CO₂ fixing enzyme), were determined over the entire water column along a latitudinal transect in the Atlantic from 64°N to 50°S covering six oceanic provinces. The abundance of aprA and cbbM genes significantly increased with depth reaching the highest abundances in meso- and upper bathypelagic layers. The contribution of cells containing these genes also increased from mesotrophic towards oligotrophic provinces, suggesting that under nutrient limiting conditions alternative energy sources are advantageous. However, the aprA/cbbM ratios indicated that only a fraction of the SOP is associated with inorganic carbon fixation. The aprA harbouring prokaryotic community was dominated by Pelagibacterales in surface and mesopelagic waters, while Candidatus Thioglobus, Chromatiales and the Deltaproteobacterium_SCGC dominated the bathypelagic realm. Noticeably, the contribution of the SRP to the prokaryotic community harbouring aprA gene was low, suggesting a major utilization of inorganic sulfur compounds either as an energy source (occasionally coupled with inorganic carbon fixation) or in biosynthesis pathways.     

Water-mass influences on summer Antarctic phytoplankton biomass and community structure

The association between the variability of phytoplankton biomass and community structure and the distribution of water masses around the Antarctic Peninsula were examined during austral summer 1993. Phytoplankton biomass showed high variability, and was dominated by an autotrophic flagellate (Cryptomonas sp.) that represented, on average, 91% of total phytoplankton biomass. The lowest phytoplankton biomasses were associated with the strongly mixed, saline, cold waters characteristic of the Weddell Sea water mass, and with the waters influenced by ice melt from the Bellingshausen Sea. The highest biomasses were found in the confluence of these water masses, where a front develops. Community composition also differed among water masses, with eukariotic picoplankton and diatoms having their highest relative contribution to community biomass in stations with Bellingshausen Sea and Weddell Sea water masses, whereas the abundance of Cryptomonas sp. was highest at the confluence of these waters. These results indicate that mesoscale processes, that determine water mass distribution, are of paramount importance in controlling the time and space variability of Antarctic phytoplankton.