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Although free-living (FL) and particle-attached (PA) bacteria are recognized as ecologically distinct compartments of marine microbial food-webs, few, if any, studies have determined their dynamics in abundance, function (production, respiration and substrate utilization) and taxonomy over a yearly cycle. In the Baltic Sea, abundance and production of PA bacteria (defined as the size-fraction >3.0 μm) peaked over 3 months in summer (6 months for FL bacteria), largely coinciding with blooms of Chitinophagales (Bacteroidetes). Pronounced changes in the growth efficiency (range 0.05–0.27) of FL bacteria (defined as the size-fraction

Bacteria and archaea are key contributors to deep-sea biogeochemical cycles and food webs. The disruptions these microbial communities may experience during and following polymetallic nodule mining in the Clarion-Clipperton Zone (CCZ) of the North Pacific Ocean could therefore have broad ecological effects. Our goals in this synthesis are to characterize the current understanding of biodiversity and biogeography of bacteria and archaea in the CCZ and to identify gaps in the baseline data and sampling approaches, prior to the onset of mining in the region. This is part of a large effort to compile biogeographic patterns in the CCZ, and to assess the representivity of no-mining Areas of Particular Environmental Interest, across a range of taxa. Here, we review published studies and an additional new dataset focused on 16S ribosomal RNA (rRNA) gene amplicon characterization of abyssal bacterial and archaeal communities, particularly focused on spatial patterns. Deep-sea habitats (nodules, sediments, and bottom seawater) each hosted significantly different microbial communities. An east-vs.-west CCZ regional distinction was present in nodule communities, although the magnitude was small and likely not detectable without a high-resolution analysis. Within habitats, spatial variability was driven by differences in relative abundances of taxa, rather than by abundant taxon turnover. Our results further support observations that nodules in the CCZ have distinct archaeal communities from those in more productive surrounding regions, with higher relative abundances of presumed chemolithoautotrophic Nitrosopumilaceae suggesting possible trophic effects of nodule removal. Collectively, these results indicate that bacteria and archaea in the CCZ display previously undetected, subtle, regional-scale biogeography. However, the currently available microbial community surveys are spatially limited and suffer from sampling and analytical differences that frequently confound inter-comparison; making definitive management decisions from such a limited dataset could be problematic. We suggest a number of future research priorities and sampling recommendations that may help to alleviate dataset incompatibilities and to address challenges posed by rapidly advancing DNA sequencing technology for monitoring bacterial and archaeal biodiversity in the CCZ. Most critically, we advocate for selection of a standardized 16S rRNA gene amplification approach for use in the anticipated large-scale, contractor-driven biodiversity monitoring in the region.

Marine bacterioplankton are essential in global nutrient cycling and organic matter turnover. Time-series analyses, often at monthly sampling frequencies, have established the paramount role of abiotic and biotic variables in structuring bacterioplankton communities and productivities. However, fine-scale seasonal microbial activities, and underlying biological principles, are not fully understood. We report results from four consecutive years of high-frequency time-series sampling in the Baltic Proper. Pronounced temporal dynamics in most investigated microbial variables were observed, including bacterial heterotrophic production, plankton biomass, extracellular enzyme activities, substrate uptake rate constants of glucose, pyruvate, acetate, amino acids, and leucine, as well as nutrient limitation bioassays. Spring blooms consisting of diatoms and dinoflagellates were followed by elevated bacterial heterotrophic production and abundances. During summer, bacterial productivity estimates increased even further, coinciding with an initial cyanobacterial bloom in early July. However, bacterial abundances only increased following a second cyanobacterial bloom, peaking in August. Uptake rate constants for the different measured carbon compounds varied seasonally and inter-annually and were highly correlated to bacterial productivity estimates, temperature, and cyanobacterial abundances. Further, we detected nutrient limitation in response to environmental conditions in a multitude of microbial variables, such as elevated productivities in nutrient bioassays, changes in enzymatic activities, or substrate preferences. Variations among biotic variables often occurred on time scales of days to a few weeks, yet often spanning several sampling occasions. Such dynamics might not have been captured by sampling at monthly intervals, as compared to more predictable transitions in abiotic variables such as temperature or nutrient concentrations. Our study indicates that high resolution analyses of microbial biomass and productivity parameters can help out in the development of biogeochemical and food web models disentangling the microbial black box.

Bacterioplankton communities regulate energy and matter fluxes fundamental to all aquatic life. The Baltic Sea offers an outstanding ecosystem for interpreting causes and consequences of bacterioplankton community composition shifts resulting from environmental disturbance. Yet, a systematic synthesis of the composition of Baltic Sea bacterioplankton and their responses to natural or human-induced environmental perturbations is lacking. We review current research on Baltic Sea bacterioplankton dynamics in situ (48 articles) and in laboratory experiments (38 articles) carried out at a variety of spatiotemporal scales. In situ studies indicate that the salinity gradient sets the boundaries for bacterioplankton composition, whereas, regional environmental conditions at a within-basin scale, including the level of hypoxia and phytoplankton succession stages, may significantly tune the composition of bacterial communities. Also the experiments show that Baltic Sea bacteria are highly responsive to environmental conditions, with general influences of e.g. salinity, temperature and nutrients. Importantly, nine out of ten experiments that measured both bacterial community composition and some metabolic activities showed empirical support for the sensitivity scenario of bacteria—i.e., that environmental disturbance caused concomitant change in both community composition and community functioning. The lack of studies empirically testing the resilience scenario, i.e., experimental studies that incorporate the long-term temporal dimension, precludes conclusions about the potential prevalence of resilience of Baltic Sea bacterioplankton. We also outline outstanding questions emphasizing promising applications in incorporating bacterioplankton community dynamics into biogeochemical and food-web models and the lack of knowledge for deep-sea assemblages, particularly bacterioplankton structure-function relationships. This review emphasizes that bacterioplankton communities rapidly respond to natural and predicted human-induced environmental disturbance by altering their composition and metabolic activity. Unless bacterioplankton are resilient, such changes could have severe consequences for the regulation of microbial ecosystem services.

Marine bacteria regulate fluxes of matter and energy essential for pelagic and benthic organisms and may also be involved in the formation and maintenance of commercially valuable abyssal polymetallic nodules. Future mining of these nodule fields is predicted to have substantial effects on biodiversity and physicochemical conditions in mined areas. Yet, the identity and distributions of bacterial populations in deep-sea sediments and associated polymetallic nodules has received relatively little attention. We examined bacterial communities using high-throughput sequencing of bacterial 16S rRNA gene fragments from samples collected in the water column, sediment, and polymetallic nodules in the Pacific Ocean (bottom depth ≥4,000 m) in the eastern Clarion-Clipperton Zone. Operational taxonomic units (OTUs; defined at 99% 16S rRNA gene identity) affiliated with JTB255 (Gammaproteobacteria) and Rhodospirillaceae (Alphaproteobacteria) had higher relative abundances in the nodule and sediment habitats compared to the water column. Rhodobiaceae family and Vibrio OTUs had higher relative abundance in nodule samples, but were less abundant in sediment and water column samples. Bacterial communities in sediments and associated with nodules were generally similar; however, 5,861 and 6,827 OTUs found in the water column were retrieved from sediment and nodule habitats, respectively. Cyanobacterial OTUs clustering among Prochlorococcus and Synechococcus were detected in both sediments and nodules, with greater representation among nodule samples. Such results suggest that vertical export of typically abundant photic-zone microbes may be an important process in delivery of water column microorganisms to abyssal habitats, potentially influencing the structure and function of communities in polymetallic nodule fields.

Future climate scenarios in the Baltic Sea project an increase of cyanobacterial bloom frequency and duration, attributed to eutrophication and climate change. Some cyanobacteria can be toxic and their impact on ecosystem services is relevant for a sustainable sea. Yet, there is limited understanding of the mechanisms regulating cyanobacterial diversity and biogeography. Here we unravel successional patterns and changes in cyanobacterial community structure using a two-year monthly time-series during the productive season in a 100 km coastal-offshore transect using microscopy and high-throughput sequencing of 16S rRNA gene fragments. A total of 565 cyanobacterial OTUs were found, of which 231 where filamentous/colonial and 334 picocyanobacterial. Spatial differences in community structure between coastal and offshore waters were minor. An epidemic population structure (dominance of a single cluster) was found for Aphanizomenon/Dolichospermum within the filamentous/colonial cyanobacterial community. In summer, this cluster simultaneously occurred with opportunistic clusters/OTUs e.g. Nodularia spumigena and Pseudanabaena. Picocyanobacteria, Synechococcus/Cyanobium, formed a consistent but highly diverse group. Overall, the potential drivers structuring summer cyanobacterial communities were temperature and salinity. However, the different responses to environmental factors among and within genera suggest high niche specificity for individual OTUs. The recruitment and occurrence of potentially toxic filamentous/colonial clusters was likely related to disturbance such as mixing events and short-term shifts in salinity, and not solely dependent on increasing temperature and nitrogen-limiting conditions. Nutrients did not explain further the changes in cyanobacterial community composition. Novel occurrence patterns were identified as a strong seasonal succession revealing a tight coupling between the emergence of opportunistic picocyanobacteria and the bloom of filamentous/colonial clusters. These findings highlight that if environmental conditions can partially explain the presence of opportunistic picocyanobacteria, microbial and trophic interactions with filamentous/colonial cyanobacteria should also be considered as potential shaping factors for single-celled communities. Regional climate change scenarios in the Baltic predict environmental shifts leading to higher temperature and lower salinity; conditions identified here as favorable for opportunistic filamentous/colonial cyanobacteria. Altogether, the diversity and complexity of cyanobacterial communities reported here is far greater than previously known, emphasizing the importance of microbial interactions between filamentous and picocyanobacteria in the context of environmental disturbances.

Anthropogenically induced changes in precipitation are projected to generate increased river runoff to semi-enclosed seas, intensifying loads of terrestrial dissolved organic matter and decreasing salinity. To determine how bacterial community structure and functioning adjust to such changes, we designed microcosm transplant experiments with Baltic Proper (salinity 7.2) and Bothnian Sea (salinity 3.6) water. Baltic Proper bacteria generally reached higher abundance than Bothnian Sea bacteria in both Baltic Proper and Bothnian Sea water, indicating a higher adaptability. Moreover, Baltic Proper bacteria growing in Bothnian Sea water consistently showed highest bacterial production and beta-glucosidase activity. These metabolic responses were accompanied by basin-specific changes in bacterial community structure. For example, Baltic Proper Pseudomonas and Limnobacter populations increased markedly in relative abundance in Bothnian Sea water, indicating replacement. In contrast, Roseobacter and Rheinheimera populations were stable or increased in abundance when challenged by either of the waters, indicating adjustment. Transplants to Bothnian Sea water triggered the initial emergence of particular Burkholderiaceae populations, and transplants to Baltic Proper water triggered Alteromonadaceae populations. Notably, in the subsequent re-transplant experiment, the original triggering, or priming effect, resulted in further increases to dominance of these populations. Correlated changes in community composition and metabolic activity were observed only in the transplant experiment, and only at relatively high phylogenetic resolution. This suggested an importance of successional progression for interpreting relationships between bacterial community composition and functioning. We infer that priming effects on bacterial community structure by natural episodic events or climate change induced forcing could translate into long-term changes in bacterial ecosystem process rates.