Bacterial communities in larger islands have reduced temporal turnover

Species turnover within cystic fibrosis lung microbiota is indicative of acute pulmonary exacerbation onset

BACKGROUND

Acute pulmonary exacerbations (PEx) are associated with increased morbidity and earlier mortality for people living with cystic fibrosis (pwCF). The most common causes of PEx in CF are by bacterial infection and concomitant inflammation leading to progressive airway damage. To draw attention to the seriousness of PEx they have been labelled as 'lung attacks', much like a 'heart attack' for acute myocardial infarction. Treatment typically starts when a pwCF presents with worsening respiratory symptoms. Hence, there is a pressing need to identify indicative biomarkers of PEx onset to allow more timely intervention. Set within an ecological framework, we investigated temporal microbiota dynamics to connect changes in the lung microbiota of pwCF to changes in disease states across a PEx event.

RESULTS

Species-time relationships (STR) describe how the richness of a community changes with time, here STRs were used to assess temporal turnover (w) within the lung microbiota of each pwCF (n = 12, mean sample duration 315.9 ± 42.7 days). STRs were characterised by high interpatient variability, indicating that turnover and hence temporal organization are a personalized feature of the CF lung microbiota. Greater turnover was found to be significantly associated with greater change in lung function with time. When microbiota turnover was examined at a finer scale across each pwCF time series, w-values could clearly be observed to increase in the exacerbation period, then peaking within the treatment period, demonstrating that increases in turnover were not solely a result of perturbations caused by PEx antibiotic interventions. STR w-values have been found to have a remarkable degree of similarity for different organisms, in a variety of habitats and ecosystems, and time lengths (typically not exceeding w = 0.5). Here, we found w-values soon increased beyond that. It was therefore possible to use the departure from that expected norm up to start of treatment to approximate onset of PEx in days (21.2 ± 8.9 days across the study participants).

CONCLUSIONS

Here, we illustrate that changes in turnover of the lung microbiota of pwCF can be indicative of PEx onset in considerable advance of when treatment would normally be initiated. This offers translational potential to enable early detection of PEx and consequent timely intervention. Video Abstract.

Replicating community dynamics reveals how initial composition shapes the functional outcomes of bacterial communities

Bacterial communities play key roles in global biogeochemical cycles, industry, agriculture, human health, and animal husbandry. There is therefore great interest in understanding bacterial community dynamics so that they can be controlled and engineered to optimise ecosystem services. We assess the reproducibility and predictability of bacterial community dynamics by creating a frozen archive of hundreds of naturally-occurring bacterial communities that we repeatedly revive and track in a standardised, complex resource environment. Replicate communities follow reproducible trajectories and the community dynamics closely map to ecosystem functioning. However, even under standardised conditions, the communities exhibit tipping-points, where small differences in initial community composition create divergent compositional and functional outcomes. The predictability of community trajectories therefore requires detailed knowledge of rugged compositional landscapes where ecosystem properties are not the inevitable result of prevailing environmental conditions but can be tilted toward different outcomes depending on the initial community composition. Our results shed light on the relationship between composition and function, opening new avenues to understand the feasibility and limitations of function prediction in complex microbial communities.

Interpreting Microbial Species-Area Relationships: Effects of Sequence Data Processing Algorithms and Fitting Models

In the study of Species-Area Relationships (SARs) in microorganisms, outcome discrepancies primarily stem from divergent high-throughput sequencing data processing algorithms and their combinations with different fitting models. This paper investigates the impacts and underlying causes of using diverse sequence data processing algorithms in microbial SAR studies, as well as compatibility issues that arise between different algorithms and fitting models. The findings indicate that the balancing strategies employed by different algorithms can result in variations in the calculations of alpha and beta diversity, thereby influencing the SARs of microorganisms. Crucially, incompatibilities exist between algorithms and models, with no consistently optimal combination identified. Based on these insights, we recommend prioritizing the use of the DADA2 algorithm in conjunction with a power model, which demonstrates greater compatibility. This study serves as a comprehensive comparison and reference for fundamental methods in microbial SAR research. Future microbial SAR studies should carefully select the most appropriate algorithms and models based on specific research objectives and data structures.

Slower but deeper community change: Intrinsic dynamics regulate anthropogenic impacts on species temporal turnover

Understanding the mechanisms behind biodiversity dynamics is central to assessing and forecasting anthropogenic impacts on ecological communities. However, the manner in which external environmental drivers act in concert with intrinsic ecological processes to influence local temporal turnover is currently largely unexplored. Here, we determine how human impacts affect multiple metrics of bird community turnover to establish the ecological mechanisms behind compositional change. We used US Breeding Bird Survey data to calculate transect-level rates of three measures of temporal species turnover: (1) "short-term" (initial rate of decline of Sørensen similarity), (2) "long-term" (asymptotic Sørensen similarity), and (3) "throughput" (overall species accumulation rate from species-time relationship exponents) over 2692 transects across 27 regional habitat types. We then hierarchically fit linear models to estimate the effect of anthropogenic impact on these turnover metrics, using the Human Modification Index proxy, while accounting for observed species richness, the size of the species pool, and annual environmental variability. We found broadly consistent impacts of increased anthropogenic pressures across diverse habitat types. The Human Modification Index was associated with greater turnover at long timescales, but marginally slower short-term turnover. The species "throughput" (accumulation rate) was not notably influenced. Examining anthropogenic impacts on different aspects of species turnover in combination allows greater ecological insight. Observed human impacts on short-term turnover were the opposite of existing expectations and suggest humans are disrupting the background turnover of these systems, rather than simply driving rapid directed turnover. The increased long-term turnover without concurrent increases in species accumulation implies human impacts lead to shifts in species occurrence frequency rather than simply greater arrival of "new" species. These results highlight the role of intrinsic dynamics and caution against simple interpretations of increased species turnover as reflections of environmental change.

Dissipation of pesticides and responses of bacterial, fungal and protistan communities in a multi-contaminated vineyard soil

The effect of pesticide residues on non-target microorganisms in multi-contaminated soils remains poorly understood. In this study, we examined the dissipation of commonly used pesticides in a multi-contaminated vineyard soil and its effect on bacterial, fungal, and protistan communities. We conducted laboratory soil microcosm experiments under varying temperature (20°C and 30°C) and water content (20 % and 40 %) conditions. Pesticide dissipation half-lives ranged from 27 to over 300 days, depending on the physicochemical properties of the pesticides and the soil conditions. In both autoclaved and non-autoclaved soil experiments, over 50 % of hydrophobic pesticides (dimethomorph > isoxaben > simazine = atrazine = carbendazim) dissipated within 200 days at 20°C and 30°C. However, the contribution of biodegradation to the overall dissipation of soluble pesticides (rac-metalaxyl > isoproturon = pyrimethanil > S-metolachlor) increased to over 75 % at 30°C and 40 % water content. This suggests that soluble pesticides became more bioavailable, with degradation activity increasing with higher temperature and soil water content. In contrast, the primary process contributing to the dissipation of hydrophobic pesticides was sequestration to soil. High-throughput amplicon sequencing analysis indicated that water content, temperature, and pesticides had domain-specific effects on the diversity and taxonomic composition of bacterial, fungal, and protistan communities. Soil physicochemical properties had a more significant effect than pesticides on the various microbial domains in the vineyard soil. However, pesticide exposure emerged as a secondary factor explaining the variations in microbial communities, with a more substantial effect on protists compared to bacterial and fungal communities. Overall, our results highlight the variability in the dissipation kinetics and processes of pesticides in a multi-contaminated vineyard soil, as well as their effects on bacterial, fungal, and protistan communities.

Time is of the essence: A general framework for uncovering temporal structures of communities

Ecological communities are inherently dynamic: species constantly turn over within years, months, weeks or even days. These temporal shifts in community composition determine essential aspects of species interactions and how energy, nutrients, information, diseases and perturbations 'flow' through systems. Yet, our understanding of community structure has relied heavily on static analyses not designed to capture critical features of this dynamic temporal dimension of communities. Here, we propose a conceptual and methodological framework for quantifying and analysing this temporal dimension. Conceptually, we split the temporal structure into two definitive features, sequence and duration, and review how they are linked to key concepts in ecology. We then outline how we can capture these definitive features using perspectives and tools from temporal graph theory. We demonstrate how we can easily integrate ongoing research on phenology into this framework and highlight what new opportunities arise from this approach to answer fundamental questions in community ecology. As climate change reshuffles ecological communities worldwide, quantifying the temporal organization of communities is imperative to resolve the fundamental processes that shape natural ecosystems and predict how these systems may change in the future.

Inoculation with adapted bacterial communities promotes development of full scale slow sand filters for drinking water production

Gravity-driven filtration through slow sand filters (SSFs) is one of the oldest methods for producing drinking water. As water passes through a sand bed, undesired microorganisms and chemicals are removed by interactions with SSF biofilm and its resident microbes. Despite their importance, the processes through which these microbial communities form are largely unknown, as are the factors affecting these processes. In this study, two SSFs constructed using different sand sources were compared to an established filter and observed throughout their maturation process. One SSF was inoculated through addition of sand scraped from established filters, while the other was not inoculated. The operational and developing microbial communities of SSFs, as well as their influents and effluents, were studied by sequencing of 16S ribosomal rRNA genes. A functional microbial community resembling that of the established SSF was achieved in the inoculated SSF, but not in the non-inoculated SSF. Notably, the non-inoculated SSF had significantly (p < 0.01) higher abundances of classes Armatimonadia, Elusimicrobia, Fimbriimonadia, OM190 (phylum Planctomycetota), Parcubacteria, Vampirivibrionia and Verrucomicrobiae. Conversely, it had lower abundances of classes Anaerolineae, Bacilli, bacteriap25 (phylum Myxococcota), Blastocatellia, Entotheonellia, Gemmatimonadetes, lineage 11b (phylum Elusimicrobiota), Nitrospiria, Phycisphaerae, subgroup 22 (phylum Acidobacteriota) and subgroup 11 (phylum Acidobacteriota). Poor performance of neutral models showed that the assembly and dispersal of SSF microbial communities was mainly driven by selection. The temporal turnover of microbial species, as estimated through the scaling exponent of the species-time relationship, was twice as high in the non-inoculated filter (0.946 ± 0.164) compared to the inoculated filter (0.422 ± 0.0431). This study shows that the addition of an inoculum changed the assembly processes within SSFs. Specifically, the rate at which new microorganisms were observed in the biofilm was reduced. The reduced temporal turnover may be driven by inoculating taxa inhibiting growth, potentially via secondary metabolite production. This in turn would allow the inoculation community to persist and contribute to SSF function.

Ecological patterns and processes of temporal turnover within lung infection microbiota

BACKGROUND

Chronic infection and consequent airway inflammation are the leading causes of morbidity and early mortality for people living with cystic fibrosis (CF). However, lower airway infections across a range of chronic respiratory diseases, including in CF, do not follow classical 'one microbe, one disease' concepts of infection pathogenesis. Instead, they are comprised of diverse and temporally dynamic lung infection microbiota. Consequently, temporal dynamics need to be considered when attempting to associate lung microbiota with changes in disease status. Set within an island biogeography framework, we aimed to determine the ecological patterns and processes of temporal turnover within the lung microbiota of 30 paediatric and adult CF patients prospectively sampled over a 3-year period. Moreover, we aimed to ascertain the contributions of constituent chronic and intermittent colonizers on turnover within the wider microbiota.

RESULTS

The lung microbiota within individual patients was partitioned into constituent chronic and intermittent colonizing groups using the Leeds criteria and visualised with persistence-abundance relationships. This revealed bacteria chronically infecting a patient were both persistent and common through time, whereas intermittently infecting taxa were infrequent and rare; respectively representing the resident and transient portions of the wider microbiota. It also indicated that the extent of chronic colonization was far greater than could be appreciated with microbiological culture alone. Using species-time relationships to measure temporal turnover and Vellend's rationalized ecological processes demonstrated turnover in the resident chronic infecting groups was conserved and underpinned principally by the deterministic process of homogenizing dispersal. Conversely, intermittent colonizing groups, representing newly arrived immigrants and transient species, drove turnover in the wider microbiota and were predominately underpinned by the stochastic process of drift. For adult patients, homogenizing dispersal and drift were found to be significantly associated with lung function. Where a greater frequency of homogenizing dispersal was observed with worsening lung function and conversely drift increased with better lung function.

CONCLUSIONS

Our work provides a novel ecological framework for understanding the temporal dynamics of polymicrobial infection in CF that has translational potential to guide and improve therapeutic targeting of lung microbiota in CF and across a range of chronic airway diseases. Video Abstract.

A genus in the bacterial phylum Aquificota appears to be endemic to Aotearoa-New Zealand

Allopatric speciation has been difficult to examine among microorganisms, with prior reports of endemism restricted to sub-genus level taxa. Previous microbial community analysis via 16S rRNA gene sequencing of 925 geothermal springs from the Taupō Volcanic Zone (TVZ), Aotearoa-New Zealand, revealed widespread distribution and abundance of a single bacterial genus across 686 of these ecosystems (pH 1.2-9.6 and 17.4-99.8 °C). Here, we present evidence to suggest that this genus, Venenivibrio (phylum Aquificota), is endemic to Aotearoa-New Zealand. A specific environmental niche that increases habitat isolation was identified, with maximal read abundance of Venenivibrio occurring at pH 4-6, 50-70 °C, and low oxidation-reduction potentials. This was further highlighted by genomic and culture-based analyses of the only characterised species for the genus, Venenivibrio stagnispumantis CP.B2T, which confirmed a chemolithoautotrophic metabolism dependent on hydrogen oxidation. While similarity between Venenivibrio populations illustrated that dispersal is not limited across the TVZ, extensive amplicon, metagenomic, and phylogenomic analyses of global microbial communities from DNA sequence databases indicates Venenivibrio is geographically restricted to the Aotearoa-New Zealand archipelago. We conclude that geographic isolation, complemented by physicochemical constraints, has resulted in the establishment of an endemic bacterial genus.

Distinct Ecological Processes Mediate Domain-Level Differentiation in Microbial Spatial Scaling

The spatial scaling of biodiversity, such as the taxa-area relationship (TAR) and distance-decay relationship (DDR), is a typical ecological pattern that is followed by both microbes and macrobes in natural ecosystems. Previous studies focusing on microbes mainly aimed to address whether and how different types of microbial taxa differ in spatial scaling patterns, leaving the underlying mechanisms largely untouched. In this study, the spatial scaling of different microbial domains and their associated ecological processes in an intertidal zone were comparatively investigated. The significant spatial scaling of biodiversity could be observed across all microbial domains, including archaea, bacteria, fungi, and protists. Among them, archaea and fungi were found with much stronger DDR slopes than those observed in bacteria and protists. For both TAR and DDR, rare subcommunities were mainly responsible for the observed spatial scaling patterns, except for the DDR of protists and bacteria. This was also evidenced by extending the TAR and DDR diversity metrics to Hill numbers. Further statistical analyses demonstrated that different microbial domains were influenced by different environmental factors and harbored distinct local community assembly processes. Of these, drift was mainly responsible for the compositional variations of bacteria and protists. Archaea were shaped by strong homogeneous selection, whereas fungi were more affected by dispersal limitation. Such differing ecological processes resulted in the domain-level differentiation of microbial spatial scaling. This study links ecological processes with microbial spatial scaling and provides novel mechanistic insights into the diversity patterns of microbes that belong to different trophic levels. IMPORTANCE As the most diverse and numerous life form on Earth, microorganisms play indispensable roles in natural ecological processes. Revealing their diversity patterns across space and through time is of essential importance to better understand the underlying ecological mechanisms controlling the distribution and assembly of microbial communities. However, the diversity patterns and their underlying ecological mechanisms for different microbial domains and/or trophic levels require further exploration. In this study, the spatial scaling of different microbial domains and their associated ecological processes in a mudflat intertidal zone were investigated. The results showed different spatial scaling patterns for different microbial domains. Different ecological processes underlie the domain-level differentiation of microbial spatial scaling. This study links ecological processes with microbial spatial scaling to provide novel mechanistic insights into the diversity patterns of microorganisms that belong to different trophic levels.

Comparative analysis of floc characteristics and microbial communities in anoxic and aerobic suspended growth processes

A fully anoxic suspended growth process is an appealing alternative to conventional activated sludge (AS) due to considerable aeration reduction and improved carbon processing efficiency for biological nutrient removal (BNR). With development of the hybrid membrane aerated biofilm reactor (MABR) technology, implementation of a fully anoxic suspended growth community in BNR facilities became practical. To better understand potential limitations with the elimination of aeration, we carried out microscopic examination and 16S rRNA gene-based microbial community profiling to determine how an anoxic suspended growth would differ from the conventional aerobic process in floc characteristics, microbial diversity, microbial temporal dynamics, and community assembly pattern. Fewer filamentous populations were found in the anoxic mixed liquor, suggesting easily sheared flocs. The anoxic microbial community had distinct composition and structure, but its diversity and temporal dynamics were similar to the conventional aerobic community. A variety of well-studied functional guilds were also identified in the anoxic community. The anoxic microbial community assembly was more stochastic than the conventional aerobic community, but deterministic assembly was still significant with a large core microbiome adapted to the anoxic condition. PRACTITIONER POINTS: Flocs developed under the anoxic conditions had less filamentous backbones, implying reduced flocculation capacity and easily sheared flocs. Knowledge about the ecophysiology of Thauera, Thiothrix, and Trichococcus can help achieve good properties of the anoxic flocs. A diverse microbial community sustainably adapted to the fully anoxic condition, containing a variety of filaments, denitrifiers, and PAOs. The anoxic microbial community displayed a similar degree of diversity and temporal dynamics compared to the aerobic counterpart. The anoxic community's assembly was more stochastic, so it may be less subject to changes in environmental variables.