Specific detection and quantification of the marine flavobacterial genus Zobellia on macroalgae using novel qPCR and CARD-FISH assays

The flavobacterial genus Zobellia is considered as a model to study macroalgal polysaccharide degradation. The lack of data regarding its prevalence and abundance in coastal habitats constitutes a bottleneck to assess its ecological strategies. To overcome this issue, real-time quantitative PCR (qPCR) and fluorescence in situ hybridization (FISH) methods targeting the 16S rRNA gene were optimized to specifically detect and quantify Zobellia on the surface of diverse macroalgae. The newly designed qPCR primers and FISH probes targeted 98 and 100% of the Zobellia strains in silico and their specificity was confirmed using pure bacterial cultures. The dynamic range of the qPCR assay spanned 8 orders of magnitude from 10 to 10⁸ 16S rRNA gene copies and the detection limit was 0.01% relative abundance of Zobellia in environmental samples. Zobellia-16S rRNA gene copies were detected on all surveyed brown, green and red macroalgae, in proportion varying between 0.1 and 0.9% of the total bacterial copies. The absolute and relative abundance of Zobellia varied with tissue aging on the kelp Laminaria digitata. Zobellia cells were successfully visualized in Ulva lactuca and stranded Palmaria palmata surface biofilm using CARD-FISH, representing in the latter 10⁵ Zobellia cells·cm⁻² and 0.43% of total bacterial cells. Overall, qPCR and CARD-FISH assays enabled robust detection, quantification and localization of Zobellia representatives in complex samples, underlining their ecological relevance as primary biomass degraders potentially cross-feeding other microorganisms.     

Seasonal niche differentiation among closely related marine bacteria

Bacteria display dynamic abundance fluctuations over time in marine environments, where they play key biogeochemical roles. Here, we characterized the seasonal dynamics of marine bacteria in a coastal oligotrophic time series station, tested how similar the temporal niche of closely related taxa is, and what are the environmental parameters modulating their seasonal abundance patterns. We further explored how conserved the niche is at higher taxonomic levels. The community presented recurrent patterns of seasonality for 297 out of 6825 amplicon sequence variants (ASVs), which constituted almost half of the total relative abundance (47%). For certain genera, niche similarity decreased as nucleotide divergence in the 16S rRNA gene increased, a pattern compatible with the selection of similar taxa through environmental filtering. Additionally, we observed evidence of seasonal differentiation within various genera as seen by the distinct seasonal patterns of closely related taxa. At broader taxonomic levels, coherent seasonal trends did not exist at the class level, while the order and family ranks depended on the patterns that existed at the genus level. This study identifies the coexistence of closely related taxa for some bacterial groups and seasonal differentiation for others in a coastal marine environment subjected to a strong seasonality.Subject terms: Microbial ecology, Microbial ecology     

Seasonality of biogeochemically relevant microbial genes in a coastal ocean microbiome

Microbes drive the biogeochemical cycles of marine ecosystems through their vast metabolic diversity. While we have a fairly good understanding of the spatial distribution of these metabolic processes in various ecosystems, less is known about their seasonal dynamics. We investigated the annual patterns of 21 biogeochemical relevant functions in an oligotrophic coastal ocean site by analysing the presence of key genes, analysing high-rank gene taxonomy and the dynamics of nucleotide variants. Most genes presented seasonality: photoheterotrophic processes were enriched during spring, phosphorous-related genes were dominant during summer, coinciding with potential phosphate limitation, and assimilatory nitrate reductases appeared mostly during summer and autumn, correlating negatively with nitrate availability. Additionally, we identified the main taxa driving each function at each season and described the role of underrecognized taxa such as Litoricolaceae in carbon fixation (rbcL), urea degradation (ureC), and CO oxidation (coxL). Finally, the seasonality of single variants of some families presented a decoupling between the taxonomic abundance patterns and the functional gene patterns, implying functional specialization of the different genera. Our study unveils the seasonality of key biogeochemical functions and the main taxonomic groups that harbour these relevant functions in a coastal ocean ecosystem.     

Allelochemicals produced by Caribbean macroalgae and cyanobacteria have species-specific effects on reef coral microorganisms

Coral populations have precipitously declined on Caribbean reefs while algal abundance has increased, leading to enhanced competitive damage to corals, which likely is mediated by the potent allelochemicals produced by both macroalgae and benthic cyanobacteria. Allelochemicals may affect the composition and abundance of coral-associated microorganisms that control host responses and adaptations to environmental change, including susceptibility to bacterial diseases. Here, we demonstrate that extracts of six Caribbean macroalgae and two benthic cyanobacteria have both inhibitory and stimulatory effects on bacterial taxa cultured from the surfaces of Caribbean corals, macroalgae, and corals exposed to macroalgal extracts. The growth of 54 bacterial isolates was monitored in the presence of lipophilic and hydrophilic crude extracts derived from Caribbean macroalgae and cyanobacteria using 96-well plate bioassays. All 54 bacterial cultures were identified by ribotyping. Lipophilic extracts from two species of Dictyota brown algae inhibited >50% of the reef coral bacteria assayed, and hydrophilic compounds from Dictyota menstrualis particularly inhibited Vibrio bacteria, a genus associated with several coral diseases. In contrast, both lipo- and hydrophilic extracts from 2 species of Lyngbya cyanobacteria strongly stimulated bacterial growth. The brown alga Lobophora variegata produced hydrophilic compounds with broad-spectrum antibacterial effects, which inhibited 93% of the bacterial cultures. Furthermore, bacteria cultured from different locations (corals vs. macroalgae vs. coral surfaces exposed to macroalgal extracts) responded differently to algal extracts. These results reveal that extracts from macroalgae and cyanobacteria have species-specific effects on the composition of coral-microbial assemblages, which in turn may increase coral host susceptibility to disease and result in coral mortality.     

Linkages between bacterioplankton community composition, heterotrophic carbon cycling and environmental conditions in a highly dynamic coastal ecosystem

We used mesocosm experiments to study the bacterioplankton community in a highly dynamic coastal ecosystem during four contrasting periods of the seasonal cycle: winter mixing, spring phytoplankton bloom, summer stratification and autumn upwelling. A correlation approach was used in order to measure the degree of coupling between the dynamics of major bacterial groups, heterotrophic carbon cycling and environmental factors. We used catalysed reporter deposition-fluorescence in situ hybridization to follow changes in the relative abundance of the most abundant groups of bacteria (Alphaproteobacteria, Gammaproteobacteria and Bacteroidetes). Bacterial carbon flux-related variables included bacterial standing stock, bacterial production and microbial respiration. The environmental factors included both, biotic variables such as chlorophyll-a concentration, primary production, phytoplankton extracellular release, and abiotic variables such as the concentration of dissolved inorganic and organic nutrients. Rapid shifts in the dominant bacterial groups occurred associated to environmental changes and bacterial bulk functions. An alternation between Alphaproteobacteria and Bacteroidetes was observed associated to different phytoplankton growth phases. The dominance of the group Bacteroidetes was related to high bacterial biomass and production. We found a significant, non-spurious, linkage between the relative abundances of major bacterial groups and bacterial carbon cycling. Our results suggest that bacteria belonging to these major groups could actually share a function in planktonic ecosystems.     

大型海藻的营养盐代谢及其与近岸海域富营养化的关系

大型海藻是近岸海域重要的初级生产者,近年来人们愈来愈认识到大型海藻在近岸海域富营养化生物修复中的重要性,同时,富营养化也可能招致某些机会主义大型海藻种类的爆发生长,因此,进一步理解大型海藻与营养盐供应变化的关系就显得非常重要。本文从大型海藻营养盐代谢与海水中营养盐供应变化(主要是富营养化)的生理生态关系角度对相关问题进行评述,主要包括影响大型海藻营养盐吸收特性的重要因素、海水中营养盐的供应及大型海藻对营养盐的细胞贮存、大型海藻对营养盐的生态需求、大型海藻对近岸海域富营养化的生态响应等问题。文章还对今后的研究提出了展望。     

Macroecology meets macroevolution: evolutionary niche dynamics in the seaweed Halimeda

Aim Because of their broad distribution in geographical and ecological dimensions, seaweeds (marine macroalgae) offer great potential as models for marine biogeographical inquiry and exploration of the interface between macroecology and macroevolution. This study aims to characterize evolutionary niche dynamics in the common green seaweed genus Halimeda, use the observed insights to gain understanding of the biogeographical history of the genus and predict habitats that can be targeted for the discovery of species of special biogeographical interest. Location Tropical and subtropical coastal waters. Methods The evolutionary history of the genus is characterized using molecular phylogenetics and relaxed molecular clock analysis. Niche modelling is carried out with maximum entropy techniques and uses macroecological data derived from global satellite imagery. Evolutionary niche dynamics are inferred through application of ancestral character state estimation. Results A nearly comprehensive molecular phylogeny of the genus was inferred from a six‐locus dataset. Macroecological niche models showed that species distribution ranges are considerably smaller than their potential ranges. We show strong phylogenetic signal in various macroecological niche features. Main conclusions The evolution of Halimeda is characterized by conservatism for tropical, nutrient‐depleted habitats, yet one section of the genus managed to invade colder habitats multiple times independently. Niche models indicate that the restricted geographical ranges of Halimeda species are not due to habitat unsuitability, strengthening the case for dispersal limitation. Niche models identified hotspots of habitat suitability of Caribbean species in the eastern Pacific Ocean. We propose that these hotspots be targeted for discovery of new species separated from their Caribbean siblings since the Pliocene rise of the Central American Isthmus.     

Diversity of carbon use strategies in a kelp forest community: implications for a high CO2 ocean

Mechanisms for inorganic carbon acquisition in macroalgal assemblages today could indicate how coastal ecosystems will respond to predicted changes in ocean chemistry due to elevated carbon dioxide (CO₂). We identified the proportion of noncalcifying macroalgae with particular carbon use strategies using the natural abundance of carbon isotopes and pH drift experiments in a kelp forest. We also identified all calcifying macroalgae in this system; these were the dominant component of the benthos (by % cover) at all depths and seasons while cover of noncalcareous macroalgae increased at shallower depths and during summer. All large canopy‐forming macroalgae had attributes suggestive of active uptake of inorganic carbon and the presence of a CO₂ concentration mechanism (CCM). CCM species covered, on average, 15–45% of the benthos and were most common at shallow depths and during summer. There was a high level of variability in carbon isotope discrimination within CCM species, probably a result of energetic constraints on active carbon uptake in a low light environment. Over 50% of red noncalcifying species exhibited values below ?30‰ suggesting a reliance on diffusive CO₂ uptake and no functional CCM. Non‐CCM macroalgae covered on average 0–8.9% of rock surfaces and were most common in deep, low light habitats. Elevated CO₂ has the potential to influence competition between dominant coralline species (that will be negatively affected by increased CO₂) and noncalcareous CCM macroalgae (neutral or positive effects) and relatively rare (on a % cover basis) non‐CCM species (positive effects). Responses of macroalgae to elevated CO₂ will be strongly modified by light and any responses are likely to be different at times or locations where energy constrains photosynthesis. Increased growth and competitive ability of noncalcareous macroalgae alongside negative impacts of acidification on calcifying species could have major implications for the functioning of coastal reef systems at elevated CO₂ concentrations.     

Reproductive strategies of epialgal bryozoans

Summary

Bryozoans are common encrusting organisms in many shallow-water marine environments. Although reproducing sexually, their success as space occupiers resides largely in their capacity for colonial growth by zooidal budding (regarded by some as a form of asexual reproduction). This paper examines the reproductive strategies of several bryozoan species commonly associated with the fronds of coastal macroalgae. These range from ephemeral species that grow rapidly, reproduce and die (Electra pilosa, Celleporella hyalina, Membranipora membranacea) to more or less annual species with well-developed reproductive and growth cycles (Flustrellidra hispida, Alcyonidium spp.). Whilst many of these bryozoans brood relatively few short-lived lecithotrophic larvae, others produce large numbers of longer-lived planktotrophic larvae. The seasonal and daily patterns of larval release are described for selected species. Resource allocation to sexual and colonial functions is considered in the context of environment-genotype interactions. Reproductive strategy is especially important in determining dispersal and colonising ability, and these in turn are major determinants of ecological pattern in epialgal bryozoan communities.     

Ocean warming enhances respiration and carbon demand of coastal microbial plankton

The increase of anthropogenic CO₂ during this century is expected to cause warming of large regions of the ocean. Microbes lead the biological role in the CO₂ balance of marine ecosystems, their activity is known to be influenced by temperature, and it is important to constrain and quantify these effects on bacterial carbon use. Furthermore, if warming were to enhance the carbon demand (production + respiration) of planktonic microbes but would maintain their efficiency low (as it generally is), then most carbon consumed would end up respired. We designed a strategy in which we measured bacterial production and respiration throughout a seasonal cycle in a coastal Mediterranean site, and determined experimentally the effects of ca. 2.5 °C on these processes. We show that warming will increase nearly 20% the total carbon demand of coastal microbial plankton without any effect on their (commonly low) growth efficiency, which could generate a positive feedback between coastal warming and CO₂ production.     

Active Bacterial Populations and Grazing Impact Revealed by an In Situ Experiment in a Shallow Aquifer

To elucidate bacterial population dynamics in an aquifer, we attempted to reveal the impact of protozoan grazing on bacterial productivity and community structure by an in situ incubation experiment using a diffusion chamber. The abundance and vertical distribution of bacteria and protozoa in the aquifer were revealed using wells that were drilled in a sedimentary rock system in Itako, Ibaraki, Japan. The water column in the wells possessed aerobic and anaerobic layers. Active bacterial populations under the grazing pressure of protozoa were revealed through in situ incubation with grazer eliminating experiment by the filtration. On August 19, 2003, the total number of bacteria (TDC) decreased from 1.5 × 10⁶ cells ml^{? 1} at 2.2 m depth to 3.0 × 10⁵ cells ml^{? 1} at 10 m depth. The relative contribution of the domain Bacteria to TDC ranged between 63% and 84%. Protozoa existed at a density of 4.2 × 10⁴ to 1.9 × 10⁵ cells ml^{? 1} in both aerobic and microaerobic conditions. A grazing elimination experiment in situ for 6 days brought about clearly different bacterial community profiles between the 2.2 m and 10 m samples. The bacterial composition of the initial community was predominantly β- and γ -proteobacteria at 2.2 m, while at 10 m β-, α - and γ -proteobacteria represented 56%, 26% and 13% of the community, respectively. The distribution of bacterial abundance, community composition and growth rates in the subsurface were influenced by grazing as well as by geochemical factors (dissolved oxygen and concentrations of organic carbon, methane and sulfate). Results of the in situ incubation experiment suggested that protozoan grazing contributes significantly to bacterial population dynamics.     

BACTERIA THAT INDUCE MORPHOGENESIS IN ULVA PERTUSA (CHLOROPHYTA) GROWN UNDER AXENIC CONDITIONS1

Marine foliaceous green macroalgae such as Ulva lose their typical morphology when cultured aseptically in defined synthetic media. However, after reinfection by certain marine bacteria (isolated from unialgal cultures of Ulva pertusa Kjellman), the organisms regain their typical foliaceous or tubular morphology. To investigate the morphogenesis (MG) induced in U. pertusa by bacteria, we isolated and identified bacteria with MG activity on U. pertusa and studied the distribution of such bacteria in seawater and on various marine macroalgae. We isolated 1555 bacterial strains from 18 species of marine macroalgae (six Chlorophyta, five Phaeophyta, and seven Rhodophyta), from seawater and from sediment collected at the beach at Omaezaki, Shizuoka Prefecture; Japan. Of these, 676 bacterial strains (43.5%) showed MG activity. They were classified into six bacterial groups, Flavobacterium, Vibrio, Pseudomonas, Deleya, Escherichia, and gram-positive cocci. These bacteria were ubiquitous among the samples and were not specific to U. pertusa. Several plant growth regulators had no MG activity. Filter-sterilized supernatants of culture media of MG-active bacteria strains did not induce MG. Cocultivation of Ulva with active bacterial strains is so far the only way to induce the MG effect, which suggests that for MG direct contact between Ulva and the bacterial strain is necessary.     

Seasonal changes in the abundance and distribution of submerged aquatic vegetation in a highly managed coastal lagoon

The inflow of fresh water into coastal lagoons is a key factor influencing the structure and function of these ecosystems. Biscayne Bay, a coastal lagoon adjacent to the city of Miami, is located downstream of the Everglades ecosystem where the extensive water management system now in place has modified the historical hydrology, replacing groundwater and overland flows with pulsed releases from canals. In areas where canals discharge directly into littoral habitats, an environment with low-mean salinity and high-salinity variability is created. In this study, we characterize the salinity patterns of nearshore habitats (<500 m from shore) and document patterns of seasonal abundance and distribution of submerged aquatic vegetation (SAV) to evaluate the impacts of water management practices. Seagrasses were the principal component of the SAV community during the 2005 dry season (mean cover = 25.5%), while macroalgae dominated during the wet season (mean cover = 33.4%). The distribution and abundance of SAV were directly related to the tolerance of each taxon to salinity patterns. Seagrass species with high tolerance to low and variable salinity such as Halodule wrightii and Ruppia maritima were found only in canal-influenced areas and increased in abundance and spatial distribution in the wet season when freshwater inflow is highest. The dominance of rhizophytic macroalgae during the wet season was determined by the appearance and high abundance of Chara, a taxon commonly associated with freshwater environments. Thalassia testudinum, the most abundant seagrass species, was found throughout the study region, but decreased in abundance in the canal-influenced areas during the wet season when lower, more variable salinity resulted in lowered productivity. The data presented here showed a significant relationship between salinity patterns and the seasonal abundance and distribution of SAV. These findings support the use of SAV as appropriate indicators of changes in water quality resulting from future restoration projects associated with the Everglades Restoration Plan, which will once again modify the delivery of fresh water into littoral habitats with unknown ecological consequences. Handling editor: S. M. Thomaz     

Inputs of seabird guano alter microbial growth,community composition and the phytoplankton–bacterial interactions in a coastal system

Seabird guano enters coastal waters providing bioavailable substrates for microbial plankton, but their role in marine ecosystem functioning remains poorly understood. Two concentrations of the water soluble fraction (WSF) of gull guano were added to different natural microbial communities collected in surface waters from the Ría de Vigo (NW Spain) in spring, summer, and winter. Samples were incubated with or without antibiotics (to block bacterial activity) to test whether gull guano stimulated phytoplankton and bacterial growth, caused changes in taxonomic composition, and altered phytoplankton–bacteria interactions. Alteromonadales, Sphingobacteriales, Verrucomicrobia and diatoms were generally stimulated by guano. Chlorophyll a (Chl a) concentration and bacterial abundance significantly increased after additions independently of the initial ambient nutrient concentrations. Our study demonstrates, for the first time, that the addition of guano altered the phytoplankton–bacteria interaction index from neutral (i.e. phytoplankton growth was not affected by bacterial activity) to positive (i.e. phytoplankton growth was stimulated by bacterial activity) in the low-nutrient environment occurring in spring. In contrast, when environmental nutrient concentrations were high, the interaction index changed from positive to neutral after guano additions, suggesting the presence of some secondary metabolite in the guano that is needed for phytoplankton growth, which would otherwise be supplied by bacteria.     

The effect of temperature and algal biomass on bacterial production and specific growth rate in freshwater and marine habitats

We analyzed heterotrophic, pelagic bacterial production and specific growth rate data from 57 studies conducted in fresh, marine and estuarine/coastal waters. Strong positive relationships were identified between 1) bacterial production and bacterial abundance and 2) bacterial production and algal biomass. The relationship between bacterial production and bacterial abundance was improved by also considering water temperature. The analysis of covariance model revealed consistent differences between fresh, marine and estuarine/coastal waters, with production consistently high in estuarine/coastal environments. The log-linear regression coefficient of abundance was not significantly different from 1.00, and this linear relationship permitted the use of specific growth rate (SGR in day⁻¹) as a dependent variable. A strong relationship was identified between specific growth rate and temperature. This relationship differed slightly across the three habitats. A substantial portion of the residual variation from this relationship was accounted for by algal biomass, including the difference between marine and estuarine/coastal habitats. A small but significant difference between the fresh- and saltwater habitats remained. No significant difference between the chlorophyll effect in different habitats was identified. The model of SGR against temperature and chlorophyll was much weaker for freshwater than for marine environments. For a small subset of the data set, mean cell volume accounted for some of the residual variation in SGR. Pronounced seasonality, fluctuations in nutrient quality, and variation of the grazing environment may contribute to the unexplained variation in specific growth.     

Spatio-temporal distribution patterns of the invasive macroalga Sargassum muticum within a Danish Sargassum-bed

Sargassum muticum was first observed in Scandinavia in Limfjorden (Denmark) in 1984, where it is now the most abundant and conspicuous macroalga. Despite the ecological importance of Sargassum, few studies have described seasonal patterns within Scandinavian Sargassum beds. We quantified the dynamics of macroalgae among years and seasons along a depth transect through a typical Sargassum bed in Limfjorden. The annual investigations (summer transects 1989–1999) showed a gradual increase in the dominance of Sargassum, especially at the 2–4-m depth interval. Significant seasonal dynamics in macroalgal abundance and assemblage structure were observed in this depth interval; the mean cover of Sargassum varied from ca. 5% (autumn and winter) to 25% (mid-summer). In comparison, encrusting algae had high and relatively stable covers throughout the year (ca. 20%). Other perennial macroalgae had low mean covers (<2%) characterized by a few patches of higher abundances. Except from a spring bloom, filamentous algae had low covers throughout the year. Within this relatively uniform bed, Sargassum abundance was positively related to boulders >10 cm in diameter and species richness was negatively correlated to depth and stones <10 cm in diameter, and non-correlated to other algal form-groups or grazer densities. Thus, in Limfjorden, the distribution of Sargassum is determined by large- (>6 m) and small-scale (<1 m) depth differences where low light limits Sargassum at depth, physical disturbance and sediment stress limits Sargasum in shallow waters, and the presence of stable boulder substratum facilitate Sargassum. Competition for space from other macroalgae and herbivory are probably of minor importance.     

Accumulation of detached kelp biomass in a subtidal temperate coastal ecosystem induces succession of epiphytic and sediment bacterial communities

Kelps are dominant primary producers in temperate coastal ecosystems. Large amounts of kelp biomass can be exported to the seafloor during the algal growth cycle or following storms, creating new ecological niches for the associated microbiota. Here, we investigated the bacterial community associated with the kelp Laminaria hyperborea during its accumulation and degradation on the seafloor. Kelp tissue, seawater and sediment were sampled during a 6-month in situ experiment simulating kelp detritus accumulation. Evaluation of the epiphytic bacterial community abundance, structure, taxonomic composition and predicted functional profiles evidenced a biphasic succession. Initially, dominant genera (Hellea, Litorimonas, Granulosicoccus) showed a rapid and drastic decrease in sequence abundance, probably outcompeted by algal polysaccharide-degraders such as Bacteroidia members which responded within 4 weeks. Acidimicrobiia, especially members of the Sva0996 marine group, colonized the degrading kelp biomass after 11 weeks. These secondary colonizers could act as opportunistic scavenger bacteria assimilating substrates exposed by early degraders. In parallel, kelp accumulation modified bacterial communities in the underlying sediment, notably favouring anaerobic taxa potentially involved in the sulfur and nitrogen cycles. Overall, this study provides insights into the bacterial degradation of algal biomass in situ, an important link in coastal trophic chains.     

Effects of territorial damselfish on an algal-dominated coastal coral reef

Territorial damselfish are important herbivores on coral reefs because they can occupy a large proportion of the substratum and modify the benthic community to promote the cover of food algae. However, on coastal coral reefs damselfish occupy habitats that are often dominated by unpalatable macroalgae. The aim of this study was to examine whether damselfish can maintain distinctive algal assemblages on a coastal reef that is seasonally dominated by Sargassum (Magnetic Island, Great Barrier Reef). Here, three abundant species (Pomacentrus tripunctatus, P. wardi and Stegastes apicalis) occupied up to 60% of the reef substrata. All three species promoted the abundance of food algae in their territories. The magnitudes of the effects varied among reef zones, but patterns were relatively stable over time. Damselfish appear to readily co-exist with large unpalatable macroalgae as they can use it as a substratum for promoting the growth of palatable epiphytes. Damselfish territories represent patches of increased epiphyte load on macroalgae, decreased sediment cover, and enhanced cover of palatable algal turf.     

Sea surface temperature dictates movement and habitat connectivity of Atlantic cod in a coastal fjord system

While movements of organisms have been studied across a myriad of environments, information is often lacking regarding spatio‐seasonal patterning in complex temperate coastal systems. Highly mobile fish form an integral part of marine food webs providing linkages within and among habitats, between patches of habitats, and at different life stages. We investigated how movement, activity, and connectivity patterns of Atlantic cod (Gadus morhua) are influenced by dynamic environmental conditions. Movement patterns of 39 juvenile and subadult Atlantic cod were assessed in two coastal sites in the Swedish Skagerrak for 5 months. We used passive acoustic telemetry and network analysis to assess seasonal and spatial movement patterns of cod and their relationships to different environmental factors, using statistical correlations, analysis of recurrent spatial motifs, and generalized linear mixed models. Temperature, in combination with physical barriers, precludes significant connectivity (complex motifs) within the system. Sea surface temperature had a strong influence on connectivity (node strength, degree, and motif frequency), where changes from warmer summer waters to colder winter waters significantly reduced movement activity of fish. As the seasons changed, movement of fish gradually decreased from large‐scale (km) linkages in the summer to more localized movement patterns in the winter (limited to 100s m). Certain localized areas, however, were identified as important for connectivity throughout the whole study period, likely due to these multiple‐habitat areas fulfilling functions required for foraging and shelter. This study provides new knowledge regarding inshore movement dynamics of juvenile and subadult Atlantic cod that use complex, coastal fjord systems. The findings show that connectivity, seasonal patterns in particular, should be carefully considered when selecting conservation areas to promote marine stewardship.