Prokaryotic Community Composition Research Articles

The soil microbial food web revisited: Predatory myxobacteria as keystone taxa?

Trophic interactions are crucial for carbon cycling in food webs. Traditionally, eukaryotic micropredators are considered the major micropredators of bacteria in soils, although bacteria like myxobacteria and Bdellovibrio are also known bacterivores. Until recently, it was impossible to assess the abundance of prokaryotes and eukaryotes in soil food webs simultaneously. Using metatranscriptomic three-domain community profiling we identified pro- and eukaryotic micropredators in 11 European mineral and organic soils from different climes. Myxobacteria comprised 1.5–9.7% of all obtained SSU rRNA transcripts and more than 60% of all identified potential bacterivores in most soils. The name-giving and well-characterized predatory bacteria affiliated with the Myxococcaceae were barely present, while Haliangiaceae and Polyangiaceae dominated. In predation assays, representatives of the latter showed prey spectra as broad as the Myxococcaceae. 18S rRNA transcripts from eukaryotic micropredators, like amoeba and nematodes, were generally less abundant than myxobacterial 16S rRNA transcripts, especially in mineral soils. Although SSU rRNA does not directly reflect organismic abundance, our findings indicate that myxobacteria could be keystone taxa in the soil microbial food web, with potential impact on prokaryotic community composition. Further, they suggest an overlooked, yet ecologically relevant food web module, independent of eukaryotic micropredators and subject to separate environmental and evolutionary pressures.

Linking prokaryotic community composition to carbon biogeochemical cycling across a tropical peat dome in Sarawak, Malaysia

Tropical peat swamp forest is a global store of carbon in a water-saturated, anoxic and acidic environment. This ecosystem holds diverse prokaryotic communities that play a major role in nutrient cycling. A study was conducted in which a total of 24 peat soil samples were collected in three forest types in a tropical peat dome in Sarawak, Malaysia namely, Mixed Peat Swamp (MPS), Alan Batu (ABt), and Alan Bunga (ABg) forests to profile the soil prokaryotic communities through meta 16S amplicon analysis using Illumina Miseq. Results showed these ecosystems were dominated by anaerobes and fermenters such as Acidobacteria, Proteobacteria, Actinobacteria and Firmicutes that cover 80–90% of the total prokaryotic abundance. Overall, the microbial community composition was different amongst forest types and depths. Additionally, this study highlighted the prokaryotic communities’ composition in MPS was driven by higher humification level and lower pH whereas in ABt and ABg, the less acidic condition and higher organic matter content were the main factors. It was also observed that prokaryotic diversity and abundance were higher in the more oligotrophic ABt and ABg forest despite the constantly waterlogged condition. In MPS, the methanotroph Methylovirgula ligni was found to be the major species in this forest type that utilize methane (CH4), which could potentially be the contributing factor to the low CH4 gas emissions. Aquitalea magnusonii and Paraburkholderia oxyphila, which can degrade aromatic compounds, were the major species in ABt and ABg forests respectively. This information can be advantageous for future study in understanding the underlying mechanisms of environmental-driven alterations in soil microbial communities and its potential implications on biogeochemical processes in relation to peatland management.

Composition and diversity of prokaryotic communities sampled from sponges and soft corals in Maldivian waters

AbstractIn the present study, prokaryotic communities from nine sponge species, two octocoral species, sediment and seawater were assessed from Maldivian coral reefs. All host species contained prokaryotic communities, which were distinct from those found in sediment and seawater. Certain host species, however, contained relatively high abundances of environmental OTUs, that is, OTUs recorded in sediment and/or seawater. This was particularly the case for the sponge species Svenzea novo sp. and Stylissa carteri with respect to seawater and Liosina paradoxa with respect to sediment. The sponge species Svenzea novo sp., S. carteri, L. paradoxa, Jaspis splendens and Ptilocaulis cf. spiculifer all had relatively high abundances of Proteobacteria, Cyanobacteria and Planctomycetes and relatively low evenness compared to the remaining sponge species. They also housed distinct subsets of highly abundant OTUs, which were rare or absent in other hosts, a trait they shared with the octocoral species. The aforementioned compositional traits suggest LMA status for these sponge species. The remaining species (Hyrtios erectus, Luffariella variabilis, Neopetrosia chaliniformis and Plakortis cf. kenyensis) had high relative abundances of Chloroflexi, Actinobacteria, Acidobacteria, Gemmatimonadetes, PAUC34f (or SAUL; sponge‐associated unclassified lineage) and Poribacteria, high evenness and limited compositional variation among samples, traits associated with HMA status. Our results, furthermore, confirmed the previously established classification of H. erectus as an HMA and S. carteri as a LMA species. Both octocoral species (Melithaea maldivensis and Paraminabea sp.) housed prokaryotic communities, which were compositionally distinct from sponge species and included significantly discriminating OTUs assigned to the Tenericutes, Spirochaetae and Proteobacteria phyla and the genera Mycoplasma (Tenericutes), Spirochaeta 2 (Spirochaetae) and Endozoicomonas (Proteobacteria).

Microbial community dynamics in a hatchery recirculating aquaculture system (RAS) of sole (Solea senegalensis)

Recirculating aquaculture systems (RAS) have been developed to reduce the aquaculture environmental impact and control rearing conditions. They allow water reuse by managing waste and nutrient recycling, consequently making intensive fish production compatible with environmental sustainability. A key aspect of these systems is the water treatment performed by the beneficial bacterial community of the biofilter. In this study we aim to investigate the dynamics of the prokaryotic community of a sole (Solea senegalensis) hatchery RAS in relation to the variability of water physical-chemical parameters. Samples from different matrices (water, biofilter and tank wall biofilm) were collected from several compartments of a commercial RAS. Total DNA was isolated from the different matrices and the V4-V5 region of the 16S rRNA gene was sequenced using Illumina MiSeq® platform and the output analyzed in the DADA2 pipeline using the SILVAngs database. Overall, the prokaryotic communities were dominated by Proteobacteria (12–89%) and Bacteroidetes (8–86%) and a total of 58 genera contributed with more than 3% of the relative abundance across the different samples. The most abundant genera were Tenacibaculum, Sulfitobacter, Leucothrix, Novosphingobium, Marinicella, Pseudoalteromonas, Polaribacter_2, Schleiferia and Algibacter. The prokaryotic community shifts were found to be modelled by water parameters such as salinity and pH. This study provides new knowledge on the prokaryotic community composition in different units of recirculating systems, essential for the understanding of the microbial community balance in aquaculture and represents an important tool for overall aquaculture system management.

Two different approaches of microbial community structure characterization in riverine epilithic biofilms under multiple stressors conditions: Developing molecular indicators.

Microbial communities are major players in the biogeochemical processes and ecosystem functioning of river networks. Despite their importance in the ecosystem, biomonitoring tools relying on prokaryotes are still lacking. Only a few studies have employed both metabarcoding and quantitative techniques such as catalysed reported deposition fluorescence in situ hybridization (CARD-FISH) to analyse prokaryotic communities of epilithic biofilms in river ecosystems. We intended to investigate the efficacy of both techniques in detecting changes in microbial community structure associated with environmental drivers. We report a significant correlation between the prokaryotic community composition and pH in rivers from two different geographical areas in Norway. Both CARD-FISH and metabarcoding data were following the pattern of the environmental variables, but the main feature distinguishing the community composition was the regional difference itself. Beta-dispersion analyses on both CARD-FISH abundance and metabarcoding data revealed higher accuracy of metabarcoding to differentiate regions and river systems. The CARD-FISH results showed high variability, even for samples within the same river, probably due to some unmeasured microscale ecological variability which we could not resolve. We also present a statistical method, which uses variation coefficient and overall prevalence of taxonomic groups, to detect possible biological indicators among prokaryotes using metabarcoding data. The development of new prokaryotic bioindicators would benefit from both techniques used in this study, but metabarcoding seems to be faster and more reliable than CARD-FISH for large scale bio-assessment.

Response of prokaryote community composition to riverine and atmospheric nutrients in a coastal embayment: Role of organic matter on Vibrionales

The responses of coastal microbial communities to nutrient inputs depend on the magnitude and nature of those inputs. To understand the response of prokaryote communities to contrasting levels of nutrient inputs from different sources, three nutrient addition experiments were performed in the Ría de Vigo in spring, summer, and autumn. The experiments consisted of controlled inorganic (nitrate, ammonium and phosphate), organic (glucose and a mix of 18 amino acids), and mixed (inorganic and organic); as well as natural (atmospheric and riverine) nutrient additions to surface water samples taken from the middle of the embayment and incubated for 48h, under in situ temperature and irradiance conditions. Prokaryote community DNA was collected and analyzed using high-throughput amplicon sequencing of the 16S rRNA gene. The joint addition of inorganic and organic nutrients provoked the most pronounced changes in community composition, systematically leading to great increases in the proportion of sequence reads belonging to Vibrionales, while natural amendments only caused subtle alterations. The proportion of reads assigned to the Planktomarina genus, bacteria belonging to the order Rhodobacterales, tended to increase when natural atmospheric nutrients were added. Overall, the fraction of reads belonging to the order Flavobacteriales did not show relevant changes, although the contribution of sequences affiliated to Polaribacter and Aurantivirga genera increased after atmospheric and riverine inputs in summer, and autumn. The proportion of Vibrionales reads also increased after controlled organic amendments in autumn, and to a lesser extent after riverine additions in spring and summer. In general, our findings suggest that an increasing input of nitrogenous organic matter from allochthonous sources into this coastal environment might promote the growth of potentially pathogenic bacteria belonging to the order Vibrionales.

Prokaryotic community composition and structure during Phaeocystis globosa blooms in the Beibu Gulf, China

Phaeocystis globosa blooms have become one of the major ecological issues in the Beibu Gulf, China, in recent years, resulting in a series of negative impacts on local fisheries and industry. While prokaryotes play key roles in nutrient cycling and energy flow during algal blooms, information regarding the response of the prokaryotic community during Phaeocystis blooms remains scarce. Thus, a comprehensive field study covering the onset and senescent phase of P. globosa blooms was conducted in the area from December 2016 to February 2017. The community composition was revealed with high-throughput sequencing of the 16S rRNA gene. A total of 7426 operational taxonomic units (OTUs) (97% similarity) were identified from 3132328 effective tags, with Proteobacteria, Cyanobacteria, Thaumarchaeota, Verrucomicrobia, Euryarchaeota, Actinobacteria, and Bacteroidetes being the predominant taxa. The composition and structure of particle-attached (PA) and free-living (FL) prokaryotic communities were significantly different: the PA fraction was more diverse and unstable temporally compared to the FL fraction. Variations in the composition and structure of the prokaryotic community were closely associated with major environmental variables, particularly dissolved oxygen (DO), NH4+, PO43-, and dissolved organic carbon (DOC). The presence of P. globosa may result in differences in the prokaryotic community; members of Rhodobacteraceae, Alteromonadales, Porticoccaceae, Vibrio, Flavobacteriales, and Verrucomicrobiae were the key taxa in the prokaryotic communities during the outbreak and senescent phases of P. globosa blooms. This study provides primary information on the response of prokaryotic communities during P. globosa blooms and will facilitate further study on biogeochemical processes of algal-derived organic matter in the tropical gulf.

Prokaryotic Diversity of the Composting Thermophilic Phase: The Case of Ground Coffee Compost.

Waste biomass coming from a local coffee company, which supplied burnt ground coffee after an incorrect roasting process, was employed as a starting material in the composting plant of the Experimental Station of the University of Naples Federico II at Castel Volturno (CE). The direct molecular characterization of compost using 13C-NMR spectra, which was acquired through cross-polarization magic-angle spinning, showed a hydrophobicity index of 2.7% and an alkyl/hydroxyalkyl index of 0.7%. Compost samples that were collected during the early “active thermophilic phase” (when the composting temperature was 63 °C) were analyzed for the prokaryotic community composition and activities. Two complementary approaches, i.e., genomic and predictive metabolic analysis of the 16S rRNA V3–V4 amplicon and culture-dependent analysis, were combined to identify the main microbial factors that characterized the composting process. The whole microbial community was dominated by Firmicutes. The predictive analysis of the metabolic functionality of the community highlighted the potential degradation of peptidoglycan and the ability of metal chelation, with both functions being extremely useful for the revitalization and fertilization of agricultural soils. Finally, three biotechnologically relevant Firmicutes members, i.e., Geobacillus thermodenitrificans subsp. calidus, Aeribacillus pallidus, and Ureibacillus terrenus (strains CAF1, CAF2, and CAF5, respectively) were isolated from the “active thermophilic phase” of the coffee composting. All strains were thermophiles growing at the optimal temperature of 60 °C. Our findings contribute to the current knowledge on thermophilic composting microbiology and valorize burnt ground coffee as waste material with biotechnological potentialities.

Changes in assembly processes of soil microbial communities during secondary succession in two subtropical forests

Soil microbes re-establish plant diversity and ecosystem functions after disturbance events. Deterministic and stochastic processes are expected to contribute to microbial community assembly during long-term ecosystem recovery. We characterized soil prokaryotic and fungal communities, to determine their assembly patterns, along two chronosequences with early to later successional subtropical forests. Prokaryotic and fungal community composition was more variable in early successional forests but converged in the later successional forests. The community composition was governed by deterministic processes in the early stages, while the relative influence of stochasticity increased in the later stages. Environmental factors that predicted the shift in deterministic and stochastic balance varied within and across successional stages. In particular, the compositional dissimilarity of plant communities strongly predicted the relative influences of the two processes during succession. These findings suggest that the relative influences of deterministic and stochastic processes in shaping microbial community assembly shift during secondary succession. Consequently, plant communities are important predictors of assembly processes in soil microbial communities during long-term ecosystem recovery.

Effects of increasing lime application rates on microbial diversity and community structure in paddy soils

Liming is widely used to ameliorate acidic soils. However, few studies have addressed the effects of different lime application rates on soil microbial communities. Specifically, the effects of liming on fungal communities remain largely unknown. Here, we set up a gradient of increasing lime application rates, 0, 450, 900, 1350, 1800, 2250, 3000, and 3750 kg ha−1, to investigate the effects of lime inputs on soil properties and community diversity and composition of prokaryotes and fungi in paddy soils. Our results showed that the effect of liming on soil pH improvement become insignificant when the application rate exceeded 1800 kg ha−1. Prokaryotic diversity and community composition were both significantly influenced by liming, whereas fungal communities were less responsive. Nonetheless, the promotive effects of liming on soil prokaryotic diversity declined when lime application rates exceeded 900 kg ha−1 (or pH > 6.5). Soil pH was the key factor shaping the prokaryotic community, while pH and SOM were both important in explaining the observed variation in fungal communities. Distinct responses of ammonia oxidizing archaea (AOA) lineages were also observed as pH increased. Our results provide insights into the complex responses of both prokaryotic and fungal communities to lime application in paddy soils, and suggest that the amount of lime applied is also important for maintaining a healthy and sustainable soil environment.

Cobalamin and microbial plankton dynamics along a coastal to offshore transect in the Eastern North Atlantic Ocean.

Cobalamin (B12) is an essential cofactor that is exclusively synthesized by some prokaryotes while many prokaryotes and eukaryotes require an external supply of B12. The spatial and temporal availability of B12 is poorly understood in marine ecosystems. Field measurements of B12 along with a large set of ancillary biotic and abiotic factors were obtained during three oceanographic cruises in the NW Iberian Peninsula, covering different spatial and temporal scales. B12 concentrations were remarkably low (<1.5 pM) in all samples, being significantly higher at the subsurface Eastern North Atlantic Central Water than at shallower depths, suggesting that B12 supply in this water mass is greater than demand. Multiple regression models excluded B12 concentration as predictive variable for phytoplankton biomass or production, regardless of the presence of B12-requiring algae. Prokaryote production was the best predictor for primary production, and eukaryote community composition was better correlated with prokaryote community composition than with nutritional resources, suggesting that biotic interactions play a significant role in regulating microbial communities. Interestingly, co-occurrence network analyses based on 16S and 18S rRNA sequences allowed the identification of significant associations between potential B12 producers and consumers (e.g. Thaumarchaeota and Dynophyceae, or Amylibacter and Ostreococcus respectively), which can now be investigated using model systems in the laboratory.

The Functional Evolution of Termite Gut Microbiota

Termites primarily feed on lignocellulose or soil in association with specific gut microbes. The functioning of the termite gut microbiota is partly understood in a handful of wood-feeding pest species, but remains largely unknown in other taxa, preventing a global understanding of the functional evolution of termite gut microbiota. Here, we sequenced the gut metagenomes of 145 termites and Cryptocercus kyebangensis, a representative of the sister group of termites. We show that the prokaryotic fraction of the gut microbiota of all termites possesses similar genes for carbohydrate and nitrogen metabolisms, in proportions varying with termite phylogenetic position and diet. The presence of a conserved set of gut prokaryotic genes implies that key nutritional functions were present in the ancestor of termites and Cryptocercus. Furthermore, the abundance of these genes largely correlated with the host phylogeny. Finally, we found that the adaptation to a diet of soil by some termite lineages was accompanied by a change in the stoichiometry of genes involved in important nutritional functions rather than by the acquisition of new genes and pathways. Our results reveal that the composition and function of termite gut prokaryotic communities have been remarkably conserved since termites first appeared >150 million years ago. Therefore, the “world smallest bioreactor” has been operating as a multipartite symbiosis composed of termites, archaea, bacteria, and cellulolytic flagellates since its inception.

Soil prokaryotic community shows no response to 2 years of simulated nitrogen deposition in an arid ecosystem in northwestern China.

An arid ecosystem might be sensitive to nitrogen (N) deposition, but the associated ecosystem-specific response of soil microbes is not well studied. To assess the N enrichment effects on plant and prokaryotic community diversity, we performed a two-year NH4 NO3 treatment in a desert steppe in northwestern China. Results showed that N addition increased plant aboveground biomass and decreased plant Shannon diversity. A C4 herb (Salsola collina) became dominant, and loss of legume species was observed. The concentrations of soil NH4 + -N, NO3 - -N, microbial biomass N, and the plant aboveground biomass N pool increased in contrast to total N, suggesting that the N input into the arid ecosystem might mainly be assimilated by plants and exit the ecosystem. Remarkably, the α-diversity and structure of the soil prokaryotic community did not vary even at the highest N addition rate. Structural equation modelling further found that the plant aboveground N pool counteracted the acidification effect of N deposition and maintained soil pH thus partially stabilizing the composition of prokaryotic communities in a desert steppe. These findings suggested that the plants and N loss might contribute to the lack of responsiveness of soil prokaryotic community to N deposition in a desert steppe.

Hidden heterogeneity and co-occurrence networks of soil prokaryotic communities revealed at the scale of individual soil aggregates.

Sequencing PCR‐amplified gene fragments from metagenomic DNA is a widely applied method for studying the diversity and dynamics of soil microbial communities. Typically, DNA is extracted from 0.25 to 1 g of soil. These amounts, however, neglect the heterogeneity of soil present at the scale of soil aggregates and thus ignore a crucial scale for understanding the structure and functionality of soil microbial communities. Here, we show with a nitrogen‐depleted agricultural soil the impact of reducing the amount of soil used for DNA extraction from 250 mg to approx. 1 mg to access spatial information on the prokaryotic community structure, as indicated by 16S rRNA gene amplicon analyses. Furthermore, we demonstrate that individual aggregates from the same soil differ in their prokaryotic community compositions. The analysis of 16S rRNA gene amplicon sequences from individual soil aggregates allowed us, in contrast to 250 mg soil samples, to construct a co‐occurrence network that provides insight into the structure of microbial associations in the studied soil. Two dense clusters were apparent in the network, one dominated by Thaumarchaeota, known to be capable of ammonium oxidation at low N concentrations, and the other by Acidobacteria subgroup 6, representing an oligotrophic lifestyle to obtain energy from SOC. Overall this study demonstrates that DNA obtained from individual soil aggregates provides new insights into how microbial communities are assembled.

Native plant Maireana brevifolia drives prokaryotic microbial community development in alkaline Fe ore tailings under semi-arid climatic conditions

Native pioneer plants of high environmental tolerance may be exploited as early colonisers in alkaline Fe-ore tailings to drive the development of functional prokaryotic microbial communities, which is one of the critical pedogenic processes leading to in situ soil formation in the tailings. The present study deployed high throughput Illumina Miseq sequencing, to characterise the diversity and potential functionality of prokaryotic microbial communities in the aged Fe-ore tailings and topsoils colonised by native plant species Maireana brevifolia at an Fe ore mine in Western Australia, in comparison with those in the tailings/topsoils without plants. The composition of prokaryotic microbial communities differed between the aged tailings (AT) and topsoil sites (TS). Aged tailings (AT1-AT3) contained more bacteria tolerant of alkaline/saline conditions (e.g., Alkalilimnicola sp.) and those related to Fe biogeochemical cycling (e.g., Acidiferrobacter sp., Aciditerrimonas sp.). In comparison, the prokaryotic microbial communities in the topsoil (TS) contained abundant bacteria related to N cycling (e.g., Rhizobium sp., Frankia sp.). The presence of M. brevifolia plants significantly increased the diversity of prokaryotic microbial communities in tailings and topsoil, particularly favouring the development of bacteria related to N cycling and OM degradations (e.g., Mesorhizobium sp. Paracoccus sp., Oxalicibacterium horti, and Microbacterium sp.). The variation of microbial community were mainly explained by pH, amorphous Fe, and total N, which were regulated by M. brevifolia colonisation. The beneficial roles of pioneer plants M. brevifolia in the development of prokaryotic microbial community in the alkaline Fe ore tailings may be integrated as a key factor when designing and scaling up the process of eco-engineering Fe-ore tailings into soil under semi-arid climatic conditions.

Bioaugmented Sand Filter Columns Provide Stable Removal of Pesticide Residue From Membrane Retentate

Drinking water resources, such as groundwater, are threatened by pollution. The pesticide metabolite 2,6-dichlorobenzamide (BAM) is one of the compounds frequently found in groundwater. Studies have attempted to add specific BAM-degrading bacteria to sand filters at drinking water treatment facilities. This biotechnology has shown great potential in removing BAM from contaminated water. However, the degradation potential was formerly lost after ~2–3 weeks due to a decrease of the degrader population over time. The aim of the present study was to overcome the constraints leading to loss of degraders from inoculated filters. Our approach was threefold: (1) Development of a novel inoculation strategy, (2) lowering the flowrate to reduce washout of cells, and (3) increasing the concentration of nutrients hereunder the pollutant in a smaller inlet water stream. The two latter were achieved via modifications of the inlet water by applying membrane treatment which, besides producing an ultra-pure water fraction, produced a residual water stream with nutrients including BAM concentrated in ~ten-fold reduced volume. This was done to alleviate starvation of degrader bacteria in the otherwise oligotrophic sand filters and to enable a decreased flowrate. By this approach, we achieved 100% BAM removal over a period of 40 days in sand filter columns inoculated with the BAM-degrader Aminobacter sp. MSH1. Molecular targeting of the degrader strain showed that the population of degrader bacteria persisted at high numbers throughout the sand filter columns and over the entire timespan of the experiment. 16S rRNA gene amplicon sequencing confirmed that MSH1 dominated the bacterial communities of the inoculated sand filter columns at experimental termination. The community composition of the indigenous prokaryotes, based on beta diversity, in the sand filter columns was governed by the feed water type i.e., membrane retentate or untreated water.

Prokaryotic Diversity and Distribution Along Physical and Nutrient Gradients in the Tunisian Coastal Waters (South Mediterranean Sea).

Prokaryotes play an important role in biogeochemical cycling in marine ecosystems, but little is known about their diversity and composition, and how they may contribute to the ecological functioning of coastal areas in the South Mediterranean Sea. This study investigated bacterial and archaeal community diversity in seawater samples along the Tunisian coast subject to important physicochemical disturbances. The 16S amplicon sequencing survey revealed higher prokaryotic diversity in the northern Tunisian bays than in southeastern waters (Gulf of Gabès). The major taxonomic groups identified in all samples were Alphaproteobacteria (40.9%), Gammaproteobacteria (18.7%), Marine Group II Euryarchaeota (11.3%), and Cyanobacteria (10.9%). Among them, the relative abundance of Alteromonadales, Prochlorococcus, and some clades of Pelagibacterales (SAR11) significantly differed between the northern and the southern bays, whereas no difference was observed across coastal waters in the archaeal Candidatus Poseidoniales (MGII), Synechococcus, and Pelagibacteraceae (SAR11 clade Ia), for which no relationship was observed with the environmental variables. Both Pseudoalteromonas and Alteromonas levels increased with the increasing salinity, density and nutrients (NH4+ and/or PO43–) gradients detected toward the southern waters, while the SAR11 clades Ib and IV and Prochlorococcus, decreased in the shallow, salty and nutrient-rich coastal waters of the Gulf of Gabès. Rhodobacteraceae was positively correlated with Synechococcus and chlorophyll levels, suggesting a relationship with phytoplankton biomass. The present study provides the first insights into planktonic prokaryotic community composition in the South Mediterranean Sea through the analysis of Tunisian seawaters, which may support further investigations on the role of bacterioplankton in the biogeochemistry of these ecosystems.

Ecological drivers switch from bottom-up to top-down during model microbial community successions.

Bottom-up selection has an important role in microbial community assembly but is unable to account for all observed variance. Other processes like top-down selection (e.g., predation) may be partially responsible for the unexplained variance. However, top-down processes and their interaction with bottom-up selective pressures often remain unexplored. We utilised an in situ marine biofilm model system to test the effects of bottom-up (i.e., substrate properties) and top-down (i.e., large predator exclusion via 100 µm mesh) selective pressures on community assembly over time (56 days). Prokaryotic and eukaryotic community compositions were monitored using 16 S and 18 S rRNA gene amplicon sequencing. Higher compositional variance was explained by growth substrate in early successional stages, but as biofilms mature, top-down predation becomes progressively more important. Wooden substrates promoted heterotrophic growth, whereas inert substrates' (i.e., plastic, glass, tile) lack of degradable material selected for autotrophs. Early wood communities contained more mixotrophs and heterotrophs (e.g., the total abundance of Proteobacteria and Euglenozoa was 34% and 41% greater within wood compared to inert substrates). Inert substrates instead showed twice the autotrophic abundance (e.g., cyanobacteria and ochrophyta made up 37% and 10% more of the total abundance within inert substrates than in wood). Late native (non-enclosed) communities were mostly dominated by autotrophs across all substrates, whereas high heterotrophic abundance characterised enclosed communities. Late communities were primarily under top-down control, where large predators successively pruned heterotrophs. Integrating a top-down control increased explainable variance by 7-52%, leading to increased understanding of the underlying ecological processes guiding multitrophic community assembly and successional dynamics.

Distinct co-occurrence patterns of prokaryotic community between the waters and sediments in lakes with different salinity.

Temporal variations and co-occurrence patterns of the prokaryotic community in saline lakes remain elusive. In this study, we investigated the temporal variations of the prokaryotic community in six lakes with different salinity by using Illumina sequencing. The results showed that prokaryotic community compositions exhibited temporal variations in all studied lakes, which may be partially caused by temporal fluctuations of environmental variables (e.g. salinity, temperature, total nitrogen). Salinity fluctuations exhibited stronger influences on temporal variations of prokaryotic community composition in the lakes with low salinity than in those with high salinity. Stochastic factors (i.e. neutral processes) also contributed to temporal variations of prokaryotic community composition, and their contributions decreased with increasing salinity in the studied saline lakes. Network analysis showed that prokaryotic co-occurrence networks of the studied lakes exhibited non-random topology. Salinity affected the phylogenetic composition of nodes in the studied networks. The topological features (e.g. average connectivity and modularity) of the studied networks significantly differed between lake waters and sediments. Collectively, these results expand our knowledge of the mechanisms underlying prokaryotic community assembly and co-occurrence relationships in saline lakes with different salinity.

Deciphering Linkages Between Microbial Communities and Priming Effects in Lake Sediments With Different Salinity

AbstractPriming effects (PEs) and their associated microbial drivers are not well studied in lake sediments. Here, we investigated PEs and underlying potential microbial drivers in the sediments of lakes on the Qinghai‐Tibetan Plateau (QTP). Sediments were collected from three QTP lakes with different salinity, followed by microcosm construction and subsequent incubation at in situ temperature. The sediment microcosms were amended with 13C‐labeled glucose, on which PE intensities were evaluated in the incubations on Days 7 and 42. Positive PEs were observed in all the studied lake sediment microcosms. PE intensities exhibited significantly (p &lt; 0.05) linear correlations with most of the measured physicochemical factors (e.g., salinity, sediment total nitrogen/phosphorus, and ratios of carbon:nitrogen), and such linear correlations were inverse for the early (i.e., on Day 7) and late (i.e., on Day 42) PEs. Prokaryotic and fungal community compositions significantly changed owing to glucose addition in the studied lake microcosms, suggesting that both prokaryotes and fungi may contribute to the observed PEs. Network analysis showed that the numbers of positive correlations between fungal taxa and other microorganisms increased with the enhancement of the late PE intensity, suggesting that fungi and associated co‐metabolisms may play key roles in late PEs in this study. Collectively, this study gives new insights into PE intensity and underlying microbial drivers of PE in lake sediments, and such knowledge is of great importance to understanding organic matter mineralization in lake ecosystems.