Prokaryotic Diversity Research Articles

Microbial biofilm community dynamics in five lowland streams

Stream biofilms are complex aggregates of diverse organism groups that play a vital role in global carbon and nitrogen cycles. Most of the current studies on stream biofilm focus on a limited number of organism groups (e.g., bacteria and algae), and few have included both prokaryote and eukaryote communities simultaneously. In this study, we incubated artificial substrates in five Danish lowland streams exhibiting different hydrological and physico-chemical conditions and explored the dynamics of community composition and diversity of the benthic biofilm, including both prokaryotes and eukaryotes. We found that few phyla in the prokaryote (Gammaproteobacteria and Bacteroidetes) and eukaryote (Cercozoa) communities accounted for over two-thirds of the total abundance at most of the sites. Both prokaryotic and eukaryotic diversity displayed the same temporal patterns, i.e., diversity peaked in July and January. We also found that hydrological and physico-chemical variables significantly explained the variation in the community composition at phylum level for both prokaryotes and eukaryotes. However, a large proportion of variation remained unexplained, which can be ascribed to important but unmeasured variables like light intensity and biological factors such as trophic and non-trophic interactions as revealed by network analysis. Therefore, we suggest that use of a multitrophic level perspective is needed to study biofilm i.e., the “microbial jungles”, where high occurrences of trophic and non-trophic interactions are expected.

First Insights into the Microbiology of Three Antarctic Briny Systems of the Northern Victoria Land

Different polar environments (lakes and glaciers), also in Antarctica, encapsulate brine pools characterized by a unique combination of extreme conditions, mainly in terms of high salinity and low temperature. Since 2014, we have been focusing our attention on the microbiology of brine pockets from three lakes in the Northern Victoria Land (NVL), lying in the Tarn Flat (TF) and Boulder Clay (BC) areas. The microbial communities have been analyzed for community structure by next generation sequencing, extracellular enzyme activities, metabolic potentials, and microbial abundances. In this study, we aim at reconsidering all available data to analyze the influence exerted by environmental parameters on the community composition and activities. Additionally, the prediction of metabolic functions was attempted by the phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt2) tool, highlighting that prokaryotic communities were presumably involved in methane metabolism, aromatic compound biodegradation, and organic compound (proteins, polysaccharides, and phosphates) decomposition. The analyzed cryoenvironments were different in terms of prokaryotic diversity, abundance, and retrieved metabolic pathways. By the analysis of DNA sequences, common operational taxonomic units ranged from 2.2% to 22.0%. The bacterial community was dominated by Bacteroidetes. In both BC and TF brines, sequences of the most thermally tolerant and methanogenic Archaea were detected, some of them related to hyperthermophiles.

Evaluation of Three Prokaryote Primers for Identification of Prokaryote Community Structure and Their Abode Preference in Three Distinct Wetland Ecosystems.

The ultimate role of prokaryote (bacteria and archaea), the decomposer of the wetland ecosystem, depends on its community structure and its interaction with the environment. The present study has used three universal prokaryote primers to compare prokaryote community structure and diversity of three distinctly different wetlands. The study results revealed that α-diversity indices and phylogenetic differential abundance patterns did not differ significantly among primers, but they did differ significantly across wetlands. Microbial community composition revealed a distinct pattern for each primer in each wetland. Overall comparison of prokaryote communities in sediments of three wetlands revealed the highest prokaryote richness and diversity in Bhomra (freshwater wetland) followed by Malencho (brackish-water wetland) and East Kolkata wetland (EKW) (sewage-fed wetland). Indicator genus analysis identified 21, 4, and 29 unique indicator genera, having preferential abode for Bhomra, EKW, and Malencho, respectively. Prediction of potential roles of these microbes revealed a preference for sulfate-reducing microbes in Malencho and methanogens in Bhomra. The distinct phylogenetic differential abundance pattern, microbial abode preference, and their potential functional role predict ecosystem variables shaping microbial diversity. The variation in community composition of prokaryotes in response to ecosystem variables can serve as the most sensitive bioindicator of wetland ecosystem assessment and management.

Prokaryotic diversity and potentially pathogenic bacteria in vended foods and environmental samples

PurposeReady-to-eat fast food vending outlets provide a cheap and readily available food. Foodborne diseases have been previously reported in Embu, Kenya, but data on the prokaryotic metagenome in vended foods is scanty. This study aimed to determine the prokaryotic diversity in fruits, vegetable salad, African sausage, chips (potato fries), fried fish, roasted beef (meat), smokies, samosa, soil, and water collected from food vendors and the surrounding environment in Embu Town and Kangaru Market.MethodsThe study used 454 pyrosequencing, Illumina high-throughput sequencing of 16S rRNA gene in the analysis of total community DNA extracted from samples using the phenol-chloroform method. The 16S rRNA gene variable region (V4-V7) of the extracted DNA was amplified and library construction performed. Sequence analysis was done using QIIME2. Hierarchical clustering of samples, diversity indices, rarefaction curves, and Venn diagrams were generated using the R programming language in R software version 3.6.3.ResultsBacterial operational taxonomic units (OUTs) were distributed in Proteobacteria (52.81%), Firmicutes (31.16%), and Lentisphaerae (0.001%). The OTUs among archaea were Candidatus Nitrososphaera (63.56%) and Nitrososphaera spp. (8.77%). Brucella spp. and Bacillus cereus associated with foodborne diseases were detected. Potential pathogens, Rickettsia spp. in risk group 2 and Brucella spp. in risk group 3, were detected. Uncultured Candidatus Koribacter and Candidatus Solibacter were also detected in the food samples. There was a significant difference in the microbial community structure among the sample types (P<0.1).ConclusionThe results demonstrated the presence of some prokaryotes that are associated with food spoilage or foodborne diseases in vended foods and environmental samples. This study also detected uncultured prokaryotes. The presence of potential pathogens calls for stringent hygiene measures in food vending operations.

Holocene life and microbiome profiling in ancient tropical Lake Chalco, Mexico

Metagenomic and traditional paleolimnological approaches are suitable to infer past biological and environmental changes, however, they are often applied independently, especially in tropical regions. We combined both approaches to investigate Holocene Prokaryote and Eukaryote diversity and microbial metabolic pathways in ancient Lake Chalco, Mexico. Here, we report on diversity among a large number of lineages (36,722 OTUs) and functional diversity (27,636,243 non-clustered predicted proteins, and 6,144 annotated protein-family genes). The most abundant domain is Bacteria (81%), followed by Archaea (15%) and Eukarya (3%). We also determined the diversity of protein families and their relationship to metabolic pathways. The early Holocene (> 11,000 cal years BP) lake was characterized by cool, freshwater conditions, which later became warmer and hyposaline (11,000–6,000 cal years BP). We found high abundances of cyanobacteria, and fungi groups associated with mature forests in these sediments. Bacteria and Archaea include mainly anaerobes and extremophiles that are involved in the sulfur, nitrogen, and carbon cycles. We found evidence for early human impacts, including landscape modifications and lake eutrophication, which began ~ 6,000 cal years BP. Subsaline, temperate conditions were inferred for the past 5,000 years. Finally, we found nitrogen-fixing bacteria and protein-family genes that are linked to contaminated environments, as well as several fungal pathogens of crops in near-surface sediments.

Impact of the algal-bacterial community structure, physio-types and biological and environmental interactions on the performance of a high rate algal pond treating biogas and wastewater

This study investigated the algal and prokaryotic community structure in an outdoors pilot High Rate Algal Pond (HRAP) that was simultaneously used for the treatment of high-strength wastewater and biogas upgrading. The algal and prokaryotic diversity was analyzed and correlated with biological and environmental parameters, and process quality indicators. The results obtained showed that the dominance of a versatile and resistant algae, such as Chlorella vulgaris, which is tolerant to high NH4+ and CO2 concentrations, concomitant to a specific prokaryotic population allowed for the obtention of biomethane with 95.2 ± 0.7% CH4, 1.4 ± 0.1% CO2 and no H2S. The bacterial community, fostered by the algal population, the light hours, and photoperiod had an important role on both biogas upgrading, through O2 and H2S elimination, and wastewater treatment. While the algal population was involved in the elimination of the ammonium of the wastewater through assimilation, the bacterial population was the main factor responsible for organic carbon, nitrate and phosphate removal, as well as nitrification. The low oxygen concentrations at night promoted bacterial denitrification, increasing the nitrite concentration in the treated wastewater. Through these findings, this research encourages photosynthetic biogas upgrading combined with wastewater treatment in HRAPs using an inoculum composed of a dominant microalgae, and an enriched prokaryotic population of aerobic chemo-organoheterotrophs, aerobic nitrifiers, and sulfur bacteria. Unlike the bacterial consortium in this study, this designed consortium can avoid the accumulation of nitrite in the cultivation broth and reduce the content of oxygen in the produced biomethane.

Application of Polyaluminium Chloride Coagulant in Urban River Water Treatment Influenced the Microbial Community in River Sediment

Polyaluminium chloride (PAC) has been widely used as a chemical coagulant in water treatment. However, little is known about the impact of PAC performance on the microbial community in sediments. In this study, the archaeal, bacterial, and fungal communities in urban river sediments with and without PAC treatment were investigated. Prokaryotic diversity decreased at the PAC addition site (A2) and increased along with the river flow (from A3 to A4), while eukaryotic diversity was the opposite. The abundance of core microbiota showed a similar trend. For example, the dominant Proteobacteria presented the highest relative abundance in A1 (26.8%) and the lowest in A2 (15.3%), followed by A3 (17.5%) and A4 (23.0%). In contrast, Rozellomycota was more dominant in A2 (56.6%) and A3 (58.1%) than in A1 (6.2%) and A4 (16.3%). Salinity, total dissolved solids, and metal contents were identified as the key physicochemical factors affecting the assembly of core microorganisms. The predicted functions of archaea and fungi were mainly divided into methane cycling and saprotrophic nutrition, respectively, while bacterial function was more diversified. The above findings are helpful to enhance our understanding of microorganism response to PAC and have significance for water treatment within the framework of microecology.

Microbiomes of Healthy and Bleached Corals During a 2016 Thermal Bleaching Event in the Upper Gulf of Thailand

Global warming has caused elevated seawater temperature and coral bleaching, including events on shallow reefs in the upper Gulf of Thailand (uGoT). Previous studies have reported an association between loss of zooxanthellae and coral bleaching. However, studies on the microbial diversity of prokaryotes and eukaryotes (microbiome) as coral holobionts are also important and this information is still limited in the uGoT. To address this shortcoming, this report provided baseline information on the prokaryotic (bacteria and archaea) and eukaryotic microbes of healthy and bleached colonies of four prevalent corals Acropora humilis, Acropora millepora, Platygyra sinensis, and Porites lutea and surrounding seawater and sediments, using 16S and 18S rRNA gene next-generation sequencing. Both prokaryotic and eukaryotic microbes showed isolated community profiles among sample types (corals, sediment, and seawater) (ANOSIM: P &amp;lt; 0.001, R = 0.51 for prokaryotic profiles and P &amp;lt; 0.001, R = 0.985 for eukaryotic microbe profiles). Among coral species, P. sinensis showed the most diverse prokaryotic community compared with the others (ANOSIM: P &amp;lt; 0.001, R = 0.636), and P. lutea showed the most diverse eukaryotic microbes (P = 0.014, R = 0.346). Healthy and bleached corals had some different microbiomes in species and their prevalences. For instance, the significant increase of Alphaproteobacteria in P. sinensis resulted in reduced prokaryotic community evenness and altered potential metabolic profiles (i.e., increased amino acid metabolism and genetic information processing and transcription, but decreased prokaryotic functions in cell motility, signaling, and transduction). For eukaryotic microbes, the loss of the algal Symbiodinium (colloquially known as zooxanthellae) in bleached corals such as P. lutea resulted in increased Chromista and Protista and, hence, clearly distinct eukaryotic microbe (including fungi) communities in healthy vs. bleached colonies of corals. Bleached corals were enriched in bacterial pathogens (e.g., Acinetobacter, Helicobacter, Malassesia, and Aspergillus) and decreased coral-beneficial prokaryotic and eukaryotic microbes (e.g., Rhizobiales and Symbiodinium). Additionally, this study identified microbiome species in bleached P. lutea that might help bleaching recovery (e.g., high abundance of Rhizobiales, Oceanospirillales, Flavobacteriales, and Alteromonadales). Overall, our coral-associated microbiome analyses identified altered diversity patterns of bacteria, archaea, fungi, and eukaryotic microbes between healthy and bleached coral species that are prevalent in the uGoT. This knowledge supports our ongoing efforts to manipulate microbial diversity as a means of reducing the negative impacts of thermal bleaching events in corals inhabiting the uGoT.

Impact of sample collection on prokaryotic and eukaryotic diversity of niche environments of the oil-sand mining impacted Athabasca River.

Microbial communities are an important aspect of overall riverine ecology; however, appreciation of the effects of anthropogenic activities on unique riverine microbial niches, and how the collection of these samples affects the observed diversity and community profile is lacking. We analyzed prokaryotic and eukaryotic communities from surface water, biofilms, and suspended load niches along a gradient of oil sands-related contamination in the Athabasca River (Alberta, Canada), with suspended load or particle-associated communities collected either via Kenney Sampler or centrifugation manifold. At the phylum level, different niche communities were highly similar to each other and across locations. However, there were significant differences in the abundance of specific genera among the different niches and across sampling locations. A generalized linear model revealed that use of the Kenney Sampler resulted in more diverse bacterial and eukaryotic suspended load community than centrifugal collection, though suspended load communities collected by any means remained stably diverse across locations. Although there was an influence of water quality parameters on community composition, all sampled sites support diverse bacterial and eukaryotic communities regardless of the degree of contamination, highlighting the need to look beyond ecological diversity as a means of assessing ecological perturbations, and consider collecting samples from multiple niche environments.

Temporal Microbial Community Dynamics Within a Unique Acid Saline Lake.

Lake Magic is an extremely acidic, hypersaline lake found in Western Australia, with the highest concentrations of aluminum and silica in the world. Previous studies of Lake Magic diversity have revealed that the lake hosts acid- and halotolerant bacterial and fungal species. However, they have not canvassed microbial population dynamics across flooding, evapo-concentration and desiccation stages. In this study, we used amplicon sequencing and potential function prediction on sediment and salt mat samples. We observed that the bacterial and fungal diversity in Lake Magic is strongly driven by carbon, temperature, pH and salt concentrations at the different stages of the lake. We also saw that the fungal diversity decreased as the environmental conditions became more extreme. However, prokaryotic diversity was very dynamic and bacteria dominated archaeal species, both in abundance and diversity, perhaps because bacteria better tolerate the extreme variation in conditions. Bacterial species diversity was the highest during early flooding stage and decreased during more stressful conditions. We observed an increase in acid tolerant and halotolerant species in the sediment, involved in functions such as sulfur and iron metabolism, i.e., species involved in buffering the external environment. Thus, due to activity within the microbial community, the environmental conditions in the sediment do not change to the same degree as conditions in the salt mat, resulting in the sediment becoming a safe haven for microbes, which are able to thrive during the extreme conditions of the evapo-concentration and desiccation stages.

Procaryotic Diversity and Hydrogenotrophic Methanogenesis in an Alkaline Spring (La Crouen, New Caledonia).

(1) Background: The geothermal spring of La Crouen (New Caledonia) discharges warm (42 °C) alkaline water (pH~9) enriched in dissolved nitrogen with traces of methane, but its microbial diversity has not yet been studied. (2) Methods: Cultivation-dependent and -independent methods (e.g., Illumina sequencing and quantitative PCR based on 16S rRNA gene) were used to describe the prokaryotic diversity of this spring. (3) Results: Prokaryotes were mainly represented by Proteobacteria (57% on average), followed by Cyanobacteria, Chlorofexi, and Candidatus Gracilibacteria (GN02/BD1-5) (each > 5%). Both potential aerobes and anaerobes, as well as mesophilic and thermophilic microorganisms, were identified. Some of them had previously been detected in continental hyperalkaline springs found in serpentinizing environments (The Cedars, Samail, Voltri, and Zambales ophiolites). Gammaproteobacteria, Ca. Gracilibacteria and Thermotogae were significantly more abundant in spring water than in sediments. Potential chemolithotrophs mainly included beta- and gammaproteobacterial genera of sulfate-reducers (Ca. Desulfobacillus), methylotrophs (Methyloversatilis), sulfur-oxidizers (Thiofaba, Thiovirga), or hydrogen-oxidizers (Hydrogenophaga). Methanogens (Methanobacteriales and Methanosarcinales) were the dominant Archaea, as found in serpentinization-driven and deep subsurface ecosystems. A novel alkaliphilic hydrogenotrophic methanogen (strain CAN) belonging to the genus Methanobacterium was isolated, suggesting that hydrogenotrophic methanogenesis occurs at La Crouen.

Prokaryotic and eukaryotic diversity in hydrothermal continental systems.

The term extremophile was suggested more than 30years ago and represents microorganisms that are capable of developing and living under extreme conditions, these conditions being particularly hostile to other types of microorganisms and to humankind. In terrestrial hydrothermal sites, like hot springs, "mud pools", solfataras, and geysers, the dominant extreme conditions are high temperature, low or high pH, and high levels of salinity. The diversity of microorganisms inhabiting these sites is determined by the conditions of the environment. Organisms belonging to the domains Archaea and Bacteria are more represented than the one belonging to Eukarya. Eukarya members tend to be less present because of their lower tolerance to higher temperatures, however, they perform important ecosystem processes when present. Both prokaryotes and eukaryotes have morphological and physical adaptations that allow them to colonize extreme environments. Microbial mats are complex associations of microorganisms that help the colonization of more extreme systems. In this review, a characterization of prokaryotic and eukaryotic organisms that populate terrestrial hydrothermal systems are made.

Genomics-informed insights into microbial degradation of N,N-dimethylformamide

Effective degradation of N,N-Dimethylformamide (DMF), an important industrial waste product, is challenging as only few bacterial isolates are known to degrade DMF. Aerobic remediation has typically been used, whereas anoxic remediation attempts are recently made, using nitrate as one electron acceptor, and ideally include methane as a byproduct. Here, we analyzed 20,762 complete genomes and 28 constructed draft genomes for genes associated with DMF degradation. We identified 952 genomes that harbor genes involved in DMF degradation, expanding the known diversity of prokaryotes with these metabolic capabilities. Our findings suggest plasmids play important roles in DMF degradation in the order Rhizobiales and genus Paracoccus, but not in most other lineages. Degradation pathway analysis reveals that most putative DMF degraders using aerobic Pathway I will accumulate methylamine intermediate, while around 6% of the DMF degraders that are primarily members of Paracoccus, Rhodococcus, Achromobacter, and Pseudomonas could potentially mineralize DMF completely. The aerobic DMF degradation via Pathway II is more common than thought and is primarily present in α-, and β-Proteobacteria and Actinobacteria. Around half (446/952) of putative DMF degraders could grow with nitrate anaerobically (Pathway III), however, genes for the use of methyl-CoM to produce methane were not found. These analyses suggest that microbial consortia could be more advantageous in DMF degradation than pure culture, particularly for methane production under the anaerobic condition. The identified genomes and plasmids form an important foundation for optimizing bioremediation of DMF-containing wastewaters.

Morphological and phylogenetic diversity of magnetotactic bacteria and multicellular magnetotactic prokaryotes from a mangrove ecosystem in the Sanya River, South China

Morphological and phylogenetic diversity of magnetotactic bacteria and multicellular magnetotactic prokaryotes from a mangrove ecosystem in the Sanya River, South China

Functional redundancy and specific taxa modulate the contribution of prokaryotic diversity and composition to multifunctionality.

Observational and experimental evidence has revealed the functional importance of microbial diversity. However, the effects of microbial diversity loss on ecosystem functions are not consistent across studies, which are probably tempered by microbial functional redundancy, specific taxa and functions evaluated. Here we conducted diversity manipulation experiments in two independent soils with distinct prokaryotic communities, and investigated how the initial community traits (e.g., distinct functional redundancy and taxonomic composition) modulate the contribution of prokaryotic diversity loss and composition shift to eight ecosystem functions related to soil nutrient cycling. We found that diversity loss impaired three functions (potential nitrification rate, N2 -fixation activity and phosphatase) and multifunctionality only in the communities with low functional redundancy, but all examined functions were unaffected in the communities with high functional redundancy. All significantly affected functions belonged to specialized functions, while the broad function (soil basal respiration) was unaffected. Moreover, prokaryotic composition explained more functional variation than diversity, which was ascribed to the crucial role of specific taxa that influence particular functions. Taken together, this study provides empirical evidence for identifying the mechanism underlying the ecosystem response to changes in microbial community, with implications for improving the prediction of ecosystem process models and managing microbial communities to promote ecosystem services.

Estuarine microbial diversity and nitrogen cycling increase along sand-mud gradients independent of salinity and distance.

Estuaries are depositional environments prone to terrigenous mud sedimentation. While macrofaunal diversity and nitrogen retention are greatly affected by changes in sedimentary mud content, its impact on prokaryotic diversity and nitrogen cycling activity remains understudied. We characterized the composition of estuarine tidal flat prokaryotic communities spanning a habitat range from sandy to muddy sediments, while controlling for salinity and distance. We also determined the diversity, abundance and expression of ammonia oxidizers and N2 O-reducers within these communities by amoA and clade I nosZ gene and transcript analysis. Results show that prokaryotic communities and nitrogen cycling fractions were sensitive to changes in sedimentary mud content, and that changes in the overall community were driven by a small number of phyla. Significant changes occurred in prokaryotic communities and N2 O-reducing fractions with only a 3% increase in mud, while thresholds for ammonia oxidizers were less distinct, suggesting other factors are also important for structuring these guilds. Expression of nitrogen cycling genes was substantially higher in muddier sediments, and results indicate that the potential for coupled nitrification-denitrification became increasingly prevalent as mud content increased. Altogether, results demonstrate that mud content is a strong environmental driver of diversity and N-cycling dynamics in estuarine microbial communities.

Prokaryotic diversity and activity in contrasting productivity regimes in late summer in the Kerguelen region (Southern Ocean)

Natural iron (Fe) fertilization sustains phytoplankton blooms above the Kerguelen plateau (Indian sector of the Southern Ocean) within otherwise low productive off-plateau waters. In early spring and summer, these diatom-dominated blooms are associated with distinct heterotrophic prokaryotic communities, but whether a structuring effect extends to the post-bloom period has thus far not been investigated. To address this question, we carried out a detailed study of the prokaryotic community composition in the region of Kerguelen Island during late Austral summer (18 February to 27 March 2018; MOBYDICK project). Concentrations of chlorophyll a were seasonally low above the plateau (0.27–0.58 μg Chl a L −1 ) and in a similar range to those at the 3 off-plateau sites investigated (0.14–0.34 μg Chl a L −1 ), but we observed an accumulation of dissolved organic carbon and the build-up of heterotrophic prokaryotic biomass in Kerguelen plateau waters. Illumina sequencing of the 16S rRNA gene revealed that the total (DNA-based) and potentially active (RNA-based) prokaryotic communities were structured according to on- and off-plateau sites in the wind-mixed surface layer, in both the free-living (<0.8 μm size fraction) and particle-attached (>0.8 μm size fraction) fractions. The Amplicon Sequence Variants (ASV) with significantly higher relative abundances in on-plateau surface waters as compared to off-plateau waters belonged to Halieaceae OM60 group, several Flavobacteriaceae , such as the NS5 marine group, Aurantivirga and Ulvibacter , Rhodobacteraceae Loktanella , Saprospiraceae , and the Cryomorphaceae NS10 marine group. ASVs with higher relative abundances in off-plateau waters belonged to the Flavobacteriaceae Formosa , the Rhodobacteraceae Planktomarina and the SAR11 clade. We discuss the potential abiotic and biotic drivers of community composition in late Austral summer and the ecological roles of abundant prokaryotic taxa in Kerguelen plateau waters.

Microbial-driven genetic variation in holobionts.

Genetic variation in holobionts (host and microbiome), occurring in both host and microbiome genomes, can be observed from two perspectives: observable variations and processes that bring about the variation. Observable includes the enormous genetic diversity of prokaryotes, which gave rise to eukaryotes. Holobionts then evolved a rich microbiome with a stable core containing essential genes, less so common taxa and a more diverse non-core, enabling considerable genetic variation. Thus, the human gut microbiome, for example, contains 1000 times more unique genes than are present in the human genome. Microbial-driven genetic variation processes in holobionts include: (1) acquisition of novel microbes from the environment, (2) amplification/reduction of certain microbes in the microbiome, (3) horizontal gene transfer between microbes and between microbes and host and (4) mutation, which plays a role in optimizing interactions between microbiota and between microbiota and host. We suggest that invertebrates and plants, where microbes can live intracellularly, have a greater chance of genetic exchange between microbiota and host, a greater chance of vertical transmission and a greater effect of microbiome on evolution than vertebrates. However, even in vertebrates the microbiome can aid in environmental fluctuations by amplification/reduction and by acquisition of novel microorganisms.

Belowground effects of deer in a temperate forest are time-dependent

The past century witnessed a dramatic increase in deer abundance in North America, Western Europe, and Japan, that triggered profound changes in the vegetation structure of temperate forests. Considering the effects large herbivores can have on soil properties and organisms, it is likely that such increased deer abundance will have consequences belowground. Current studies in temperate forests, however, found inconsistent results regarding the effect of deer on soils within, and across, ecosystems. These inconsistencies may be the result of a time-dependent response of the soil to deer presence. Short-term belowground modifications may reflect the direct interactions of deer on soil (i.e. trampling and waste deposition), while long-term belowground modifications may reflect both direct and indirect effects of deer on soil (e.g. through vegetation shifts). To test these ideas, we measured the effects of deer on soil properties and prokaryotic communities in the temperate forests of Haida Gwaii, Canada. We compared three complementary systems varying in duration of deer presence or exclusion, so as to be able to assess the short- (before and after a deer cull), intermediate- (inside vs. outside deer exclosures) and long- (comparing islands with and without deer) term effects of deer, respectively. We found no change in soil physical and chemical properties and in prokaryotic community structure after one year of deer removal. Twenty years of deer exclusion significantly reduced soil compaction but had no effect on soil prokaryotic community structure. Over 70 years of deer presence significantly correlated with: increased soil compaction, reduced total soil phosphorus content and soil prokaryotic diversity, and modified soil prokaryotic community structure and composition. Such effects of deer on the soil may have consequences for nutrient cycling. Revealing the belowground effects of deer in temperate forests, therefore, requires long-term studies, longer than most of those currently available in the literature.

Microeukaryotic and Prokaryotic Diversity of Anchialine Caves from Eastern Adriatic Sea Islands

Anchialine ecosystems in the eastern Adriatic Sea are diverse both morphologically and biologically. In this study, for the first time, we explored the microeukaryotic and prokaryotic community of anchialine caves in the Mediterranean region using high-throughput sequencing. Four anchialine caves located on nearby islands with a well-pronounced salinity gradient were sampled at the surface freshwater area, halocline area, and seawater area. Sequencing revealed a surprisingly wide diversity of the microeukaryotic and prokaryotic community with the relative abundance of major phyla differing within the salinity gradient and between the caves. Interestingly, microeukaryotic and prokaryotic communities clustered into four groups based on location, pointing out that sampled anchialine caves have different microbial community patterns and high microbial endemism. Our results indicate that even with the halocline acting as a selecting barrier, the salinity is not the only community structuring factor. Despite the short geographical distance, the isolation of anchialine caves facilitated high microbial community adaptation and endemism. Our study suggests that anchialine caves represent reservoirs of new biodiversity, maintaining unique and complex microbial diversity influenced by biotic interactions and abiotic environmental conditions.