Distinct Biogeographic Patterns Research Articles

Low diversity and abundance of predatory fishes in a peripheral coral reef ecosystem.

Semi-enclosed seas are often associated with elevated local threats and distinct biogeographic patterns among marine fishes, but our understanding of how fish assemblage dynamics vary in relation to relatively small semi-enclosed seas (e.g., the Gulf of Aqaba) remains limited. Baited remote underwater video surveys (n = 111) were conducted across ~300 km of coral reef habitats in the Gulf of Aqaba and the northern Red Sea. A total of 55 predatory fish species were detected, with less than half of all species (n = 23) observed in both basins. Relative abundance patterns between the Gulf of Aqaba and the northern Red Sea were variable among taxa, but nearly twice as many predatory fish were observed per unit of effort in the northern Red Sea. In general, assemblages in both basins were dominated by three taxa (Epinephelinae, Carangidae, and Lethrinidae). Large-bodied and threatened species were recorded at very low abundances. Multivariate analysis revealed distinct assemblage structuring of coral reef predators between the Gulf of Aqaba and the northern Red Sea. Most of the species driving these differences were recorded in both basins, but occurred at varying levels of abundance. Environmental factors were largely unsuccessful in explaining variation in assemblage structuring. These findings indicate that biological assemblages in the Gulf of Aqaba are more distinct than previously reported and that reef fish assemblage structuring can occur even within a relatively small semi-enclosed sea. Despite inter-basin assemblage structuring, the overall low abundance of vulnerable fish species is suggestive of overexploitation in both the Gulf of Aqaba and the northern Red Sea of Saudi Arabia. As the region surveyed is currently undergoing large-scale coastal development, the results presented herein aim to guide spatial management and recovery plans for these coral reef systems in relation to this development.

Bacterioplankton diversity and potential health risks in volcanic lakes: A study from Arxan Geopark, China

Bacterioplankton play a vital role in maintaining the functions and services of lake ecosystems. Understanding the diversity and distribution patterns of bacterioplankton, particularly the presence of potential pathogenic bacterial communities, is crucial for safeguarding human health. In this study, we employed 16S rRNA gene amplicon sequencing to investigate the diversity and geographic patterns of bacterioplankton communities, as well as potential pathogens, in eight volcanic lakes located in the Arxan UNESCO Global Geopark (in the Greater Khingan Mountains of China). Our results revealed that the bacterial communities primarily comprised Bacteroidota (45.3%), Proteobacteria (33.1%), and Actinobacteria (9.0%) at the phylum level. At the genus level, prominent taxa included Flavobacterium (31.5%), Acinetobacter (11.0%), Chryseobacterium (7.9%), and CL500-29 marine group (5.6%). Among the bacterioplankton, we identified 34 pathogen genera (165 amplicon sequence variants [ASVs]), with Acinetobacter (59.8%), Rahnella (18.3%), Brevundimonas (9.6%), and Pseudomonas (5.8%) being the most dominant. Our findings demonstrated distinct biogeographic patterns in the bacterial communities at the local scale, driven by a combination of dispersal limitation and environmental factors influenced by human activities. Notably, approximately 15.3% of the bacterioplankton reads in the Arxan lakes were identified as potential pathogens, underscoring the potential risks to public health in these popular tourist destinations. This study provides the first comprehensive insight into the diversity of bacterioplankton in mountain lake ecosystems affected by high tourist activity, laying the groundwork for effective control measures against bacterial pathogens.

Metagenome-assembled genomes reveal greatly expanded taxonomic and functional diversification of the abundant marine Roseobacter RCA cluster

BackgroundThe RCA (Roseobacter clade affiliated) cluster belongs to the family Roseobacteracea and represents a major Roseobacter lineage in temperate to polar oceans. Despite its prevalence and abundance, only a few genomes and one described species, Planktomarina temperata, exist. To gain more insights into our limited understanding of this cluster and its taxonomic and functional diversity and biogeography, we screened metagenomic datasets from the global oceans and reconstructed metagenome-assembled genomes (MAG) affiliated to this cluster.ResultsThe total of 82 MAGs, plus five genomes of isolates, reveal an unexpected diversity and novel insights into the genomic features, the functional diversity, and greatly refined biogeographic patterns of the RCA cluster. This cluster is subdivided into three genera: Planktomarina, Pseudoplanktomarina, and the most deeply branching Candidatus Paraplanktomarina. Six of the eight Planktomarina species have larger genome sizes (2.44–3.12 Mbp) and higher G + C contents (46.36–53.70%) than the four Pseudoplanktomarina species (2.26–2.72 Mbp, 42.22–43.72 G + C%). Cand. Paraplanktomarina is represented only by one species with a genome size of 2.40 Mbp and a G + C content of 45.85%. Three novel species of the genera Planktomarina and Pseudoplanktomarina are validly described according to the SeqCode nomenclature for prokaryotic genomes. Aerobic anoxygenic photosynthesis (AAP) is encoded in three Planktomarina species. Unexpectedly, proteorhodopsin (PR) is encoded in the other Planktomarina and all Pseudoplanktomarina species, suggesting that this light-driven proton pump is the most important mode of acquiring complementary energy of the RCA cluster. The Pseudoplanktomarina species exhibit differences in functional traits compared to Planktomarina species and adaptations to more resource-limited conditions. An assessment of the global biogeography of the different species greatly expands the range of occurrence and shows that the different species exhibit distinct biogeographic patterns. They partially reflect the genomic features of the species.ConclusionsOur detailed MAG-based analyses shed new light on the diversification, environmental adaptation, and global biogeography of a major lineage of pelagic bacteria. The taxonomic delineation and validation by the SeqCode nomenclature of prominent genera and species of the RCA cluster may be a promising way for a refined taxonomic identification of major prokaryotic lineages and sublineages in marine and other prokaryotic communities assessed by metagenomics approaches.4nWA41D1uUohyPVze8XWvDVideo

Climate and ant diversity explain the global distribution of ant‐plant mutualisms

Biotic interactions play an important role in shaping species geographic distributions and diversity patterns. However, the role of mutualistic interactions in shaping global plant diversity patterns remains poorly understood, particularly with respect to interactions with invertebrates. It is unclear how the nature of different mutualisms interacts with abiotic drivers and affects the distribution of mutualistic organisms. Here, we present a global‐scale biogeographic analysis of three distinct ant‐plant mutualisms, differentiating between plants bearing domatia, extrafloral nectaries (EFNs), and elaiosomes, based on comprehensive geographic distributions of ~ 19 000 flowering plants and ~ 13 000 ant species. Domatia and extrafloral nectaries involve indirect plant defences provided by ants, while elaiosomes attract ants to disperse seeds. Our results reveal distinct biogeographic patterns of different ant‐plant mutualisms, with domatium‐ and EFN‐bearing plant diversity decreasing sharply from the equator towards the poles, while elaiosome‐bearing plants prevail at mid‐latitudes. Present climate, especially mean annual temperature and precipitation, emerge as the strongest predictors of ant‐associated plant diversity. In hot and moist regions, typically the tropics, the representation of EFN‐bearing plants increases with the proportion of potential ant partners while domatium‐bearing plants show no correlation with ants. In dry regions, plants with elaiosomes are strongly linked to interacting ant seed dispersers. Our results suggest that ants in combination with climate drive the spatial variation of plants bearing domatia, extrafloral nectaries, and elaiosomes, highlighting the importance of mutualistic interactions for understanding plant biogeography.

Ecology of Endozoicomonadaceae in three coral genera across the Pacific Ocean

Health and resilience of the coral holobiont depend on diverse bacterial communities often dominated by key marine symbionts of the Endozoicomonadaceae family. The factors controlling their distribution and their functional diversity remain, however, poorly known. Here, we study the ecology of Endozoicomonadaceae at an ocean basin-scale by sampling specimens from three coral genera (Pocillopora, Porites, Millepora) on 99 reefs from 32 islands across the Pacific Ocean. The analysis of 2447 metabarcoding and 270 metagenomic samples reveals that each coral genus harbored a distinct new species of Endozoicomonadaceae. These species are composed of nine lineages that have distinct biogeographic patterns. The most common one, found in Pocillopora, appears to be a globally distributed symbiont with distinct metabolic capabilities, including the synthesis of amino acids and vitamins not produced by the host. The other lineages are structured partly by the host genetic lineage in Pocillopora and mainly by the geographic location in Porites. Millepora is more rarely associated to Endozoicomonadaceae. Our results show that different coral genera exhibit distinct strategies of host-Endozoicomonadaceae associations that are defined at the bacteria lineage level.

Organization of planktonic Tintinnina assemblages in the Atlantic Ocean

Marine plankton have different biogeographical distribution patterns. However, it is not clear how the entire plankton assemblage is composed of these species with distinct biogeographical patterns. Tintinnina (tintinnids) is single-celled planktonic protozoa commonly used as model organisms in planktonic studies. In this research, we investigated the organization of Tintinnina assemblages along the Atlantic Meridional Transect (AMT) spanning over 90 degrees of latitude during the 29th AMT cruise (2019). Tintinnina with high frequency of occurrence was classified into four biogeographic distribution patterns (equatorial, gyre, frontal, and deep Chl a maximum) according to their vertical and horizontal distribution. All species falling within each distribution pattern formed a sub-assemblage. Equatorial sub-assemblage dominated in upper waters of the equatorial zone and gyre centres. Equatorial and frontal sub-assemblages co-dominated in upper waters of the frontal zones. Deep Chlorophyll a maximum Layer (DCM) sub-assemblage dominated in the DCM waters. Some Tintinnina species with high abundance could be used as indicator species of sub-assemblages. The Tintinnina assemblages in the northern and southern hemispheres exhibited asymmetry in terms of species composition. The latitudinal gradient of Tintinnina species richness was bimodal, which was shaped by the superposition of the species number of the four sub-assemblages with latitude. The result of this study contributes to the understanding of Tintinnina assemblage in the equatorial zone and subtropical gyres of the Pacific and Indian Ocean. It is also valuable for predicting the influence of global warming on changes in Tintinnina distribution and species richness.

Dispersal limitation dominates the community assembly of abundant and rare fungi in dryland montane forests.

The assembly mechanisms and drivers of abundant and rare fungi in dryland montane forest soils remain underexplored. Therefore, in this study, we compared the distribution patterns of abundant and rare fungi and explored the factors determining their assembly processes in a dryland montane forest in China. Stronger distance-decay relationships (DDRs) were found in abundant sub-communities than in rare sub-communities. In addition, abundant fungi exhibited greater presence and wider habitat niche breadth than rare fungi. Both the null model and variation partitioning analysis indicated that dispersal limitation and environmental selection work together to govern both abundant and rare fungal assembly, while dispersal limitation plays a dominant role. Meanwhile, the relative influence of dispersal limitation and environmental selection varied between abundant and rare sub-communities, where dispersal limitation showed greater dominance in abundant fungal assembly. Mantel tests demonstrated that soil pH and phosphorus played critical roles in mediating abundant and rare fungi assembly processes, respectively. Our findings highlight that the distinct biogeographic patterns of abundant and rare fungi are driven by different assembly mechanisms, and the assembly processes of abundant and rare fungi are determined by diverse ecological drivers in dryland montane forest soils.

Biogeography and Population Divergence of Microeukaryotes Associated with Fluids and Chimneys in the Hydrothermal Vents of the Southwest Indian Ocean.

ABSTRACTDeep-sea hydrothermal vents have been proposed as oases for microbes, but microeukaryotes as key components of the microbial loop have not been well studied. Based on high-throughput sequencing and network analysis of the 18S rRNA gene, distinct biogeographical distribution patterns and impacting factors were revealed from samples in the three hydrothermal fields of the southwest Indian Ocean, where higher gene abundance of microeukaryotes appeared in chimneys. The microeukaryotes in the fluids might be explained by hydrogeochemical heterogeneity, especially that of the nitrate and silicate concentrations, while the microeukaryotes in the chimneys coated with either Fe oxides or Fe-Si oxyhydroxides might be explained by potentially different associated prokaryotic groups. Population divergence of microeukaryotes, especially clades of parasitic Syndiniales, was observed among different hydrothermal fluids and chimneys and deserves further exploration to gain a deeper understanding of the trophic relationships and potential ecological function of microeukaryotes in the deep-sea extreme ecosystems, especially in the complex deep-sea chemoautotrophic habitats.IMPORTANCE Deep-sea hydrothermal vents have been proposed as oases for microbes, but microeukaryotes as key components of the microbial loop have not been well studied. Based on high-throughput sequencing and network analysis of the 18S rRNA gene, population divergence of microeukaryotes, especially clades of parasitic Syndiniales, was observed among different hydrothermal fields. This might be attributed to the hydrogeochemical heterogeneity of fluids and to the potentially different associated prokaryotic groups in chimneys.

Biogeographical Patterns of Bacterial Communities and Their Antibiotic Resistomes in the Inland Waters of Southeast China.

ABSTRACTFreshwater ecosystems are important sources of drinking water and provide natural settings for the proliferation and dissemination of bacteria and antibiotic resistance genes (ARGs). However, the biogeographical patterns of ARGs in natural freshwaters and their relationships with the bacterial community at large scales are largely understudied. This is of specific importance because data on ARGs in environments with low anthropogenic impact is still very limited. We characterized the biogeographical patterns of bacterial communities and their ARG profiles in 24 reservoirs across southeast China using 16S rRNA gene high-throughput sequencing and high-throughput-quantitative PCR, respectively. We found that the composition of both bacterial communities and ARG profiles exhibited a significant distance-decay pattern. However, ARG profiles displayed larger differences among different water bodies than bacterial communities, and the relationship between bacterial communities and ARG profiles was weak. The biogeographical patterns of bacterial communities were simultaneously driven by stochastic and deterministic processes, while ARG profiles were not explained by stochastic processes, indicating a decoupling of bacterial community composition and ARG profiles in inland waters under relatively low-human-impact at a large scale. Overall, this study provides an overview of the biogeographical patterns and driving mechanisms of bacterial community and ARG profiles and could offer guidance and reference for the control of ARGs in drinking water sources.IMPORTANCE Antibiotic resistance has been a serious global threat to environmental and human health. The “One Health” concept further emphasizes the importance of monitoring the large-scale dissemination of ARGs. However, knowledge about the geographical patterns and driving mechanisms of bacterial communities and ARGs in natural freshwater environments is limited. This study uncovered the distinct biogeographical patterns of bacterial communities and ARG profiles in inland waters of southeast China under low-anthropogenic impact at a large scale. This study improved our understanding of ARG distribution in inland waters with emphasis on drinking water supply reservoirs, therefore providing the much-needed baseline information for future monitoring and risk assessment of ARGs in drinking water resources.

Soil pH and moisture govern the assembly processes of abundant and rare bacterial communities in a dryland montane forest.

The assembly mechanisms and ecological drivers of abundant and rare bacterial subcommunities in dryland montane forest ecosystems remain unclear. Here, we compared the biogeographic patterns of rare and abundant bacterial subcommunities and examined the ecological drivers governing their assembly processes in a dryland montane forest of China. Our results showed that a stronger relationship existed between phylogenetic turnover and spatial distance in rare subcommunities compared with that in abundant subcommunities. Null model analysis indicated that abundant subcommunities were predominantly controlled by dispersal limitation, whereas variable selection controlled rare bacterial assembly. More importantly, the balance between deterministic and stochastic processes for abundant and rare subcommunities was regulated by soil pH and soil moisture content, respectively, rather than aridity. Increasing soil moisture decreased the importance of deterministic processes for rare bacterial assembly. In abundant subcommunities, the dominance of stochastic processes was higher in neutral pH soils. Our findings suggested that divergent assembly mechanisms underlying distinct biogeographic patterns in rare and abundant bacterial subcommunities in dryland montane forests, and the assembly mechanisms of abundant and rare bacterial subcommunities were mediated by differentiated environmental factors. Our study provides a new understanding of the generation and maintenance of soil biodiversity in dryland ecosystems.

Divergent drivers determine soil bacterial β-diversity of forest and grassland ecosystems in Northwest China

The determinants of bacterial β-diversity across the large scale have been well explored, yet little is known that about how the driving factors of bacterial β-diversity differ between the forest and grassland in northwest China. Here, we comprehensively compared the biogeographic patterns and their drivers of bacterial communities in the forest and grassland. We also quantified the relative contribution of two components (replacement and nestedness components) to bacterial β-diversity. We found the significant distance-decay relationships in both two ecosystems, whereas more species turnover correlating with geographic distance was observed in forest ecosystems than grassland ecosystem, and the slope in the forest was significantly steeper than that in grassland. This suggests that bacterial diversity in forest and grassland soil exhibits distinct biogeographic and ecological patterns. More importantly, we found that soil bacterial β-diversity was mainly derived from replacement components in both two ecosystems, implying high proportion of endemic bacterial species distribute in dryland forest and grassland soil. Our results further demonstrated that environmental filtering have dominant effect on soil bacterial β-diversity in both forest and grassland. However, the relative roles of spatial processes varied between forest and grassland, where stochastic processes only have significant influence on soil bacterial β-diversity in forest but not in grassland. Among environmental factors, bacterial β-diversity and turnover components was mainly determined by water availability in grassland soil, but by soil pH in the forest soil. Taken together, our findings collectively suggest that differential ecological drivers underlie distinct biogeographic patterns of bacterial diversity in forest and grassland soil.

Temporal transcriptomes of a marine cyanopodovirus and its Synechococcus host during infection.

Marine picocyanobacteria belonging to genera Synechococcus and Prochlorococcus are genetically diverged and distributed into distinct biogeographical patterns, and both are infected by genetically closely related cyanopodoviruses. Previous studies have not fully explored whether the two virus–host systems share similar gene expression patterns during infection. Whole‐genome expression dynamics of T7‐like cyanopodovirus P‐SSP7 and its host Prochlorococcus strain MED4 have already been reported. Here, we conducted genomic and transcriptomic analyses on T7‐like cyanopodovirus S‐SBP1 during its infection on Synechococcus strain WH7803. S‐SBP1 has a latent period of 8 h and phage DNA production of 30 copies per cell. In terms of whole‐genome phylogenetic relationships and average nucleotide identity, S‐SBP1 was most similar to cyanopodovirus S‐RIP2, which also infects Synechococcus WH7803. Three hypervariable genomic islands were identified when comparing the genomes of S‐SBP1 and S‐RIP2. Single nucleotide variants were also observed in three S‐SBP1 genes, which were located within the island regions. Based on RNA‐seq analysis, S‐SBP1 genes clustered into three temporal expression classes, whose gene content was similar to that of P‐SSP7. Thirty‐two host genes were upregulated during phage infection, including those involved in carbon metabolism, ribosome components, and stress response. These upregulated genes were similar to those upregulated by Prochlorococcus MED4 in response to infection by P‐SSP7. Our study demonstrates a programmed temporal expression pattern of cyanopodoviruses and hosts during infection.

High soil pH enhances the network interactions among bacterial and archaeal microbiota in alpine grasslands of the Tibetan Plateau.

Soil functions and processes are driven by complex microbial interactions. It is, therefore, critical to understand the coexistence patterns of soil microbiota, especially in fragile alpine ecosystems. We identified biogeographic patterns in the network-level topological features of the soil microbial co-occurrence network in the Tibetan alpine grasslands, based on high-throughput sequencing. We verified that soil pH was the most important environmental variable for predicting network-level topological features of soil microbial co-occurrence networks. Associations among soil microbiota were enhanced with increasing pH (5.17-8.92), and the network was the most stable at neutral pH. Moreover, node-level topological features suggested that the archaeal operational taxonomic units, compared with bacterial operational taxonomic units, hold a central role in the co-occurrence network. Network-level topological features revealed closer connections among soil microbiota in the steppe ecosystem than in the meadow ecosystem. Therefore, our study demonstrated that soil pH served as a critical environmental filter that influenced the potential associations and ecological signature of soil microbiota in the Tibetan alpine grasslands. These findings provide a new perspective on the distinct biogeographic patterns of co-occurrence networks, to explore the ecological role of soil microbiota and thus help manage soil bacterial and archaeal communities for provisioning alpine ecosystem services.

Fungi show broader environmental thresholds in wet than dry agricultural soils with distinct biogeographic patterns

It is critical to establish response thresholds for fungal communities to global environmental change and assess the relationship between fungal diversity and nutrient cycling in soils. However, these have not yet been evaluated in agro-ecosystems. Here we report the findings of a survey across eastern China on the soil fungi and physicochemical properties in adjacent maize and rice fields. The results revealed a wider range of environmental thresholds for soil fungi in rice than maize fields. We found that the dominant fungal taxa only accounted for 0.6% of all taxa, but constituted >50% of total fungi. Based on their habitat preferences, distinct distribution maps between maize and rice fields were constructed, which indicated niche differentiation of soil fungi between dry and waterlogged soils. Rice fields showed higher fungal richness in low latitude regions, consistent with latitudinal richness patterns found in natural terrestrial ecosystems; however, no such trend was observed in maize fields. Fungal richness was positively correlated with nutrient cycling in rice soils and fungal beta diversity with nutrient cycling in maize soils. These findings provide response thresholds for fungal community change across environmental gradients, advancing our understanding of soil fungal diversity patterns in agricultural ecosystems. Differences between wetland and dryland should be taken into consideration when formulating sustainable management plans and baselines for assessments of future global change and resilience of agricultural fields.

Substrate rugosity and temperature matters: patterns of benthic diversity at tropical intertidal reefs in the SW Atlantic.

Modeling and forecasting ocean ecosystems in a changing world will require advances in observational efforts to monitor marine biodiversity. One of the observational challenges in coastal reef ecosystems is to quantify benthic and climate interactions which are key to community dynamics across habitats. Habitat complexity (i.e., substrate rugosity) on intertidal reefs can be an important variable explaining benthic diversity and taxa composition, but the association between substrate and seasonal variability is poorly understood on lateritic reefs in the South Atlantic. We asked if benthic assemblages on intertidal reefs with distinct substrate rugosity would follow similar seasonal patterns of succession following meteo-oceanographic variability in a tropical coastal area of Brazil. We combined an innovative 3D imaging for measuring substrate rugosity with satellite monitoring to monitor spatio-temporal patterns of benthic assemblages. The dataset included monthly in situ surveys of substrate cover and taxon diversity and richness, temporal variability in meteo-oceanographic conditions, and reef structural complexity from four sites on the Eastern Marine Ecoregion of Brazil. Additionally, correlation coefficients between temperature and both benthic diversity and community composition from one year of monitoring were used to project biodiversity trends under future warming scenarios. Our results revealed that benthic diversity and composition on intertidal reefs are strongly regulated by surface rugosity and sea surface temperatures, which control the dominance of macroalgae or corals. Intertidal reef biodiversity was positively correlated with reef rugosity which supports previous assertions of higher regional intertidal diversity on lateritic reefs that offer increased substrate complexity. Predicted warming temperatures in the Eastern Marine Ecoregion of Brazil will likely lead to a dominance of macroalgae taxa over the lateritic reefs and lower overall benthic diversity. Our findings indicate that rugosity is not only a useful tool for biodiversity mapping in reef intertidal ecosystems but also that spatial differences in rugosity would lead to very distinct biogeographic and temporal patterns. This study offers a unique baseline of benthic biodiversity on coastal marine habitats that is complementary to worldwide efforts to improve monitoring and management of coastal reefs.

Insights into protist diversity and biogeography in intertidal sediments sampled across a range of spatial scales

AbstractThe relative importance of different ecological processes that shape community structure is a central but poorly understood topic in protist ecology. This study used an 18S rRNA gene sequencing approach to examine the relative contributions of environmental selective (environmental filtering) and neutral processes (dispersal and ecological drift) in the community assembly of three diverse protist groups (Bacillariophyta, Cercozoa, and Ciliophora) from intertidal sediment samples spanning a geographical distance up to 12,000 km. All three protist communities exhibited similar and distinct biogeographical patterns, and followed strong distance–decay relationships at continental scale (ca. 12,000 km), regional scale (ca. 1500 km), and local scale (ca. 50 km). Network analysis showed that temperature, salinity, nitrite and nitrate nitrogen, total nitrogen, and 0.1–0.25 mm grain size together associated with 60.8%, 55.5%, and 50.0% of the OTUs, which represented 68.1%, 58.5%, and 59.2% of sequence abundances for Bacillariophyta, Cercozoa, and Ciliophora co‐occurrence networks, respectively, indicating that these environmental variables played the central roles in influencing community composition. On the other hand, a neutral community model explained 73.6%, 64.2%, and 70.2% of community variation for Bacillariophyta, Cercozoa, and Ciliophora, respectively. More importantly, variation partitioning and partial Mantel tests showed that environmental selection exhibited a slightly greater influence on Ciliophora compared to spatial factors, but both components were roughly equivalent in Bacillariophyta and Cercozoa communities. Taken together, these results demonstrate that both environmental selection and neutral processes play important roles in creating the biogeographical patterns of protist communities in intertidal sandy beach ecosystems.

The Diversity and Geographic Distribution of Cultivable Bacillus-Like Bacteria Across Black Soils of Northeast China.

Bacillus-like species are gram-positive bacteria that are ubiquitous in soils. Many of Bacillus-like bacteria are demonstrated as beneficial microbes widely used in industry and agriculture. However, the knowledge related to their diversity and distribution patterns in soils is still rudimentary. In this study, we developed a combined research method of using culture-dependent and high-throughput sequencing to investigate the composition and diversity of cultivable Bacillus-like bacterial communities across 26 soil samples obtained from the black soil zone in northeast China. Nearly all bacterial 16S rDNA sequences were classified into the order Bacillales. Fifteen genera were detected, with Bacillus, Paenibacillus, and Brevibacillus being the three most abundant genera. Although more than 2,000 OTUs were obtained across all samples, 33 OTUs were confirmed as the abundant species with a relative abundance over 5% in at least one sample. Pairwise analysis showed that the diversity of Bacillus-like bacterial communities were significantly and positively correlated with soil total carbon contents and soil sampling latitudes, which suggests that a latitudinal gradient diversity of Bacillus-like bacterial communities exists in the black soil zone. The principal coordinates analysis revealed that the Bacillus-like bacterial communities were remarkably affected by soil sampling latitudes and soil total carbon content. In general, this study demonstrated that a distinct biogeographic distribution pattern of cultivable Bacillus-like bacterial communities existed in the black soil zone, which emphasizes that the strategy of local isolation and application of beneficial Bacillus-like strains is rather important in black soil agriculture development.

Legacy of a Pleistocene bacterial community: Patterns in community dynamics through changing ecosystems

Bacterial communities are resilient to the environmental changes, yet the effect of long term ecological changes on bacterial communities remain poorly explored. To study the effect of prolonged environmental changes, a 25 m long sediment core was excavated from a paleo beach ridge located on the Cauvery delta, south east coast of India. Geological evidences suggested that the site has experienced multiple marine transgressions and regressions. The three paleosols from Vettaikaraniruppu (VKI) beach ridge, VKI-2 (2.8 m bgl; 3 kybp), VKI-5 (7.2 m bgl; 6 kybp) and VKI-14 (24.5 m bgl; 146 kybp) was chosen for bacterial community analysis based on their formation period. Bacterial community structure of paleosols was reconstructed using V3 hypervariable region of bacterial 16S rDNA targeted Illumina sequencing. The VKI-5 sediment layer which formed under marine environment contained highest bacterial diversity, and the community was a mix up of terrestrial and marine bacterial population. The final community VKI-2 exhibited an approximate structural pattern witnessed in the native bacterial community VKI-14 which formed during marine regression. Furthermore, marine transgression and regression experienced in VKI resulted in the formation of distinct biogeographic patterns.

Biogeographic Patterns and Assembly Mechanisms of Bacterial Communities Differ Between Habitat Generalists and Specialists Across Elevational Gradients.

A core issue in microbial ecology is the need to elucidate the ecological processes and underlying mechanisms involved in microbial community assembly. However, the extent to which these mechanisms differ in importance based on traits of taxa with different niche breadth is poorly understood. Here, we used high-throughput sequencing to examine the relative importance of environmental selection and stochastic processes in shaping soil bacterial sub-communities with different niche breadth (including habitat generalists, specialists and other taxa) across elevational gradients on the subalpine slope of Mount Wutai, Northern China. Our findings suggested that the composition of soil bacterial communities differed significantly different among elevational gradients. According to the niche breadth index, 10.9% of OTUs were defined as habitat generalists (B-value >8.7) and 10.0% of OTUs were defined as habitat specialists (B-value <1.5). Generalists and specialists differed distinctly in diversity and biogeographic patterns across elevational gradients. Environmental selection (deterministic processes) and spatial factors (stochastic processes) seemed to determine the assembly and biogeography of habitat generalists. However, for specialists, deterministic processes strongly influenced the distribution, while stochastic processes were not at play. Environmental drivers for generalists and specialists differed, as did their importance. Elevation, total nitrogen and pH were the main factors determining habitat generalists, and soil water content, nitrate nitrogen and pH had the strongest impacts on specialists. Moreover, variation partitioning analysis revealed that environmental selection had a much greater impact on both generalists (17.7% of pure variance was explained) and specialists (3.6%) than spatial factors. However, generalists had a much stronger response to spatial factors (2.3%) than specialists (0.3%). More importantly, null models of β-diversity suggested that specialists deviated significantly from non-neutral assembly mechanisms (relative null deviation= 0.64–0.74) relative to generalists (0.16–0.65) (P < 0.05). These results indicate that generalists and specialists are governed by different assembly mechanisms and present distinct biogeographical patterns. The large proportion of unexplained variation in specialists (93.3%) implies that very complex assembly mechanisms exist in the assembly of specialists across elevational gradients on the subalpine slope of Mount Wutai. It is essential to understand the microbial community assembly at a more refined level, and to expand the current understanding of microbial ecological mechanisms.

Biogeographic Distribution Patterns of the Archaeal Communities Across the Black Soil Zone of Northeast China.

Although archaea are ubiquitous in various environments, the knowledge gaps still exist regarding the biogeographical distribution of archaeal communities at regional scales in agricultural soils compared with bacteria and fungi. To provide a broader biogeographical context of archaeal diversity, this study quantified the abundance and community composition of archaea across the black soil zone in northeast China using real-time PCR and high-throughput sequencing (HTS) methods. Archaeal abundances across all soil samples ranged from 4.04 × 107 to 26.18 × 107 16S rRNA gene copies per gram of dry soil. Several soil factors were positively correlated with the abundances including soil pH, concentrations of total C, N, and P, and available K in soil, and soil water content. Approximately 94.2, 5.7, and 0.3% of archaeal sequences, and 31, 151, and 3 OTUs aligned within the phyla Thaumarchaeota, Euryarchaeota, and Crenarchaeota, respectively. Within the phylum of Thaumarchaeota, group 1.1b was a dominating genus accounting for an average of 87% archaeal sequences and phylogenetically classified as Nitrososphaera, a genus of ammonia oxidizing archaea. The response of dominating OTUs to environmental factors differed greatly, suggesting the physiological characteristics of different archaeal members is diversified in the black soils. Although the number of OTUs was not related with any particular soil parameters, the number of OTUs within Thaumarchaeota and Euryarchaeota was marginally related with soil pH. Archaeal community compositions differed between samples, and a Canonical correspondence analysis (CCA) analysis indicated that soil pH and the latitude of sampling locations were two dominating factors in shifting community structures. A variance partitioning analysis (VPA) analysis showed that the selected soil parameters (32%) were the largest drivers of community variation, in particular soil pH (21%), followed by geographic distances (19%). These findings suggest that archaeal communities have distinct biogeographic distribution pattern in the black soil zone and soil pH was the key edaphic factor in structuring the community compositions.