Microbiomes attached to fresh perennial ryegrass are temporally resilient and adapt to changing ecological niches

BACKGROUND

Gut microbiomes, such as the rumen, greatly influence host nutrition due to their feed energy-harvesting capacity. We investigated temporal ecological interactions facilitating energy harvesting at the fresh perennial ryegrass (PRG)-biofilm interface in the rumen using an in sacco approach and prokaryotic metatranscriptomic profiling.

RESULTS

Network analysis identified two distinct sub-microbiomes primarily representing primary (≤ 4 h) and secondary (≥ 4 h) colonisation phases and the most transcriptionally active bacterial families (i.e Fibrobacteriaceae, Selemondaceae and Methanobacteriaceae) did not interact with either sub-microbiome, indicating non-cooperative behaviour. Conversely, Prevotellaceae had most transcriptional activity within the primary sub-microbiome (focussed on protein metabolism) and Lachnospiraceae within the secondary sub-microbiome (focussed on carbohydrate degradation). Putative keystone taxa, with low transcriptional activity, were identified within both sub-microbiomes, highlighting the important synergistic role of minor bacterial families; however, we hypothesise that they may be 'cheating' in order to capitalise on the energy-harvesting capacity of other microbes. In terms of chemical cues underlying transition from primary to secondary colonisation phases, we suggest that AI-2-based quorum sensing plays a role, based on LuxS gene expression data, coupled with changes in PRG chemistry.

CONCLUSIONS

In summary, we show that fresh PRG-attached prokaryotes are resilient and adapt quickly to changing niches. This study provides the first major insight into the complex temporal ecological interactions occurring at the plant-biofilm interface within the rumen. The study also provides valuable insights into potential plant breeding strategies for development of the utopian plant, allowing optimal sustainable production of ruminants. Video Abstract.

Novelty and convergence in adaptation to whole genome duplication

Whole genome duplication (WGD) can promote adaptation but is disruptive to conserved processes, especially meiosis. Studies in Arabidopsis arenosa revealed a coordinated evolutionary response to WGD involving interacting proteins controlling meiotic crossovers, which are minimised in an autotetraploid (within-species polyploid) to avoid mis-segregation. Here we test whether this surprising flexibility of a conserved essential process, meiosis, is recapitulated in an independent WGD system, Cardamine amara, 17 million years diverged from A. arenosa. We assess meiotic stability and perform population-based scans for positive selection, contrasting the genomic response to WGD in C. amara with that of A. arenosa. We found in C. amara the strongest selection signals at genes with predicted functions thought important to adaptation to WGD: meiosis, chromosome remodelling, cell cycle, and ion transport. However, genomic responses to WGD in the two species differ: minimal ortholog-level convergence emerged, with none of the meiosis genes found in A. arenosa exhibiting strong signal in C. amara. This is consistent with our observations of lower meiotic stability and occasional clonal spreading in diploid C. amara, suggesting that nascent C. amara autotetraploid lineages were preadapted by their diploid lifestyle to survive while enduring reduced meiotic fidelity. However, in contrast to a lack of ortholog convergence, we see process-level and network convergence in DNA management, chromosome organisation, stress signalling, and ion homeostasis processes. This gives the first insight into the salient adaptations required to meet the challenges of a WGD state and shows that autopolyploids can utilize multiple evolutionary trajectories to adapt to WGD.

Transcriptional and environmental control of bacterial denitrification and N2O emissions

In oxygen-limited environments, denitrifying bacteria can switch from oxygen-dependent respiration to nitrate (NO3-) respiration in which the NO3- is sequentially reduced via nitrite (NO2-), nitric oxide (NO) and nitrous oxide (N2O) to dinitrogen (N2). However, atmospheric N2O continues to rise, a significant proportion of which is microbial in origin. This implies that the enzyme responsible for N2O reduction, nitrous oxide reductase (NosZ), does not always carry out the final step of denitrification either efficiently or in synchrony with the rest of the pathway. Despite a solid understanding of the biochemistry underpinning denitrification, there is a relatively poor understanding of how environmental signals and respective transcriptional regulators control expression of the denitrification apparatus. This minireview describes the current picture for transcriptional regulation of denitrification in the model bacterium, Paracoccus denitrificans, highlighting differences in other denitrifying bacteria where appropriate, as well as gaps in our understanding. Alongside this, the emerging role of small regulatory RNAs in regulation of denitrification is discussed. We conclude by speculating how this information, aside from providing a better understanding of the denitrification process, can be translated into development of novel greenhouse gas mitigation strategies.

Biodiversity-function relationships in methanogenic communities

Methanogenic communities play a crucial role in carbon cycling and biotechnology (anaerobic digestion), but our understanding of how their diversity, or composition in general, determines the rate of methane production is very limited. Studies to date have been correlational because of the difficulty in cultivating their constituent species in pure culture. Here, we investigate the causal link between methanogenesis and diversity in laboratory anaerobic digesters by experimentally manipulating the diversity of cultures by dilution and subsequent equilibration of biomass. This process necessarily leads to the loss of the rarer species from communities. We find a positive relationship between methane production and the number of taxa, with little evidence of functional saturation, suggesting that rare species play an important role in methane‐producing communities. No correlations were found between the initial composition and methane production across natural communities, but a positive relationship between species richness and methane production emerged following ecological selection imposed by the laboratory conditions. Our data suggest methanogenic communities show little functional redundancy, and hence, any loss of diversity—both natural and resulting from changes in propagation conditions during anaerobic digestion—is likely to reduce methane production.

DESIGN FACTORS FOR A SUCCESSFUL SHARED SPACE STREET (SSS) DESIGN

The concept of Shared Space Street (SSS) has the potential to bring many benefits to a city. Those include promotion of social interaction, the connectivity within the city for both vehicles and pedestrians, active engagement of the people with the space, walkability, vitality and street livability, better economic wealth and alike. These factors work together to improve livability, vitality of street and indirectly bring economic wealth to municipalities through increasing the footfall to shops, enhancing the health and safety of the locality and increasing the property values. Hence, this clearly is a consideration for strategic property management and relevant professionals. This concept has also been criticized for its practical issues when implemented in some parts of the world. Such issues include difficulties faced by aged people and people with disabilities, harassments faced by the cyclists, etc. This paper explores the methods and approaches that can be used to harness potential advantages of the SSS concept and to overcome its practical issues and criticisms through a detail evaluation of design driven use of space in three case studies within United Kingdom. Finally, this paper proposes a set of design factors which can be applied to a SSS design in order to ensure a successful implementation.

A Single Community Dominates Structure and Function of a Mixture of Multiple Methanogenic Communities

The ecology of microbes frequently involves the mixing of entire communities (community coalescence), for example, flooding events, host excretion, and soil tillage [1, 2], yet the consequences of this process for community structure and function are poorly understood [3-7]. Recent theory suggests that a community, due to coevolution between constituent species, may act as a partially cohesive unit [8-11], resulting in one community dominating after community coalescence. This dominant community is predicted to be the one that uses resources most efficiently when grown in isolation [11]. We experimentally tested these predictions using methanogenic communities, for which efficient resource use, quantified by methane production, requires coevolved cross-feeding interactions between species [12]. After propagation in laboratory-scale anaerobic digesters, community composition (determined from 16S rRNA sequencing) and methane production of mixtures of communities closely resembled that of the single most productive community grown in isolation. Analysis of each community's contribution toward the final mixture suggests that certain combinations of taxa within a community might be co-selected as a result of coevolved interactions. As a corollary of these findings, we also show that methane production increased with the number of inoculated communities. These findings are relevant to the understanding of the ecological dynamics of natural microbial communities, as well as demonstrating a simple method of predictably enhancing microbial community function in biotechnology, health, and agriculture [13].

A stable genetic polymorphism underpinning microbial syntrophy

Syntrophies are metabolic cooperations, whereby two organisms co-metabolize a substrate in an interdependent manner. Many of the observed natural syntrophic interactions are mandatory in the absence of strong electron acceptors, such that one species in the syntrophy has to assume the role of electron sink for the other. While this presents an ecological setting for syntrophy to be beneficial, the potential genetic drivers of syntrophy remain unknown to date. Here, we show that the syntrophic sulfate-reducing species Desulfovibrio vulgaris displays a stable genetic polymorphism, where only a specific genotype is able to engage in syntrophy with the hydrogenotrophic methanogen Methanococcus maripaludis. This 'syntrophic' genotype is characterized by two genetic alterations, one of which is an in-frame deletion in the gene encoding for the ion-translocating subunit cooK of the membrane-bound COO hydrogenase. We show that this genotype presents a specific physiology, in which reshaping of energy conservation in the lactate oxidation pathway enables it to produce sufficient intermediate hydrogen for sustained M. maripaludis growth and thus, syntrophy. To our knowledge, these findings provide for the first time a genetic basis for syntrophy in nature and bring us closer to the rational engineering of syntrophy in synthetic microbial communities.

Genome-Wide Discovery of Putative sRNAs in Paracoccus denitrificans Expressed under Nitrous Oxide Emitting Conditions

Nitrous oxide (N₂O) is a stable, ozone depleting greenhouse gas. Emissions of N₂O into the atmosphere continue to rise, primarily due to the use of nitrogen-containing fertilizers by soil denitrifying microbes. It is clear more effective mitigation strategies are required to reduce emissions. One way to help develop future mitigation strategies is to address the currently poor understanding of transcriptional regulation of the enzymes used to produce and consume N₂O. With this ultimate aim in mind we performed RNA-seq on a model soil denitrifier, Paracoccus denitrificans, cultured anaerobically under high N₂O and low N₂O emitting conditions, and aerobically under zero N₂O emitting conditions to identify small RNAs (sRNAs) with potential regulatory functions transcribed under these conditions. sRNAs are short (∼40–500 nucleotides) non-coding RNAs that regulate a wide range of activities in many bacteria. Hundred and sixty seven sRNAs were identified throughout the P. denitrificans genome which are either present in intergenic regions or located antisense to ORFs. Furthermore, many of these sRNAs are differentially expressed under high N₂O and low N₂O emitting conditions respectively, suggesting they may play a role in production or reduction of N₂O. Expression of 16 of these sRNAs have been confirmed by RT-PCR. Ninety percent of the sRNAs are predicted to form secondary structures. Predicted targets include transporters and a number of transcriptional regulators. A number of sRNAs were conserved in other members of the α-proteobacteria. Better understanding of the sRNA factors which contribute to expression of the machinery required to reduce N₂O will, in turn, help to inform strategies for mitigation of N₂O emissions.

Reliability of OperaVOX against Multidimensional Voice Program (MDVP)

OBJECTIVE

To evaluate the agreement between OperaVOX and MDVP.

DESIGN

Cross sectional reliability study.

SETTING

University teaching hospital.

METHODS

Fifty healthy volunteers and 50 voice disorder patients had supervised recordings in a quiet room using OperaVOX by the iPod's internal microphone with sampling rate of 45 kHz. A five-seconds recording of vowel/a/was used to measure fundamental frequency (F0), jitter, shimmer and noise-to-harmonic ratio (NHR). All healthy volunteers and 21 patients had a second recording. The recorded voices were also analysed using the MDVP. The inter- and intrasoftware reliability was analysed using intraclass correlation (ICC) test and Bland-Altman (BA) method. Mann-Whitney test was used to compare the acoustic parameters between healthy volunteers and patients.

RESULTS

Nine of 50 patients had severe aperiodic voice. The ICC was high with a confidence interval of >0.75 for the inter- and intrasoftware reliability except for the NHR. For the intersoftware BA analysis, excluding the severe aperiodic voice data sets, the bias (95% LOA) of F0, jitter, shimmer and NHR was 0.81 (11.32, -9.71); -0.13 (1.26, -1.52); -0.52 (1.68, -2.72); and 0.08 (0.27, -0.10). For the intrasoftware reliability, it was -1.48 (18.43, -21.39); 0.05 (1.31, -1.21); -0.01 (2.87, -2.89); and 0.005 (0.20, -0.18), respectively. Normative data from the healthy volunteers were obtained. There was a significant difference in all acoustic parameters between volunteers and patients measured by the Opera-VOX (P < 0.001) except for F0 in females (P = 0.87).

CONCLUSION

OperaVOX is comparable to MDVP and has high internal consistency for measuring the F0, jitter and shimmer of voice except for the NHR.

Comparative metatranscriptomics reveals kingdom level changes in the rhizosphere microbiome of plants

Plant-microbe interactions in the rhizosphere have important roles in biogeochemical cycling, and maintenance of plant health and productivity, yet remain poorly understood. Using RNA-based metatranscriptomics, the global active microbiomes were analysed in soil and rhizospheres of wheat, oat, pea and an oat mutant (sad1) deficient in production of anti-fungal avenacins. Rhizosphere microbiomes differed from bulk soil and between plant species. Pea (a legume) had a much stronger effect on the rhizosphere than wheat and oat (cereals), resulting in a dramatically different rhizosphere community. The relative abundance of eukaryotes in the oat and pea rhizospheres was more than fivefold higher than in the wheat rhizosphere or bulk soil. Nematodes and bacterivorous protozoa were enriched in all rhizospheres, whereas the pea rhizosphere was highly enriched for fungi. Metabolic capabilities for rhizosphere colonisation were selected, including cellulose degradation (cereals), H2 oxidation (pea) and methylotrophy (all plants). Avenacins had little effect on the prokaryotic community of oat, but the eukaryotic community was strongly altered in the sad1 mutant, suggesting that avenacins have a broader role than protecting from fungal pathogens. Profiling microbial communities with metatranscriptomics allows comparison of relative abundance, from multiple samples, across all domains of life, without polymerase chain reaction bias. This revealed profound differences in the rhizosphere microbiome, particularly at the kingdom level between plants.

Metagenomic study of the viruses of African straw-coloured fruit bats: detection of a chiropteran poxvirus and isolation of a novel adenovirus

Viral emergence as a result of zoonotic transmission constitutes a continuous public health threat. Emerging viruses such as SARS coronavirus, hantaviruses and henipaviruses have wildlife reservoirs. Characterising the viruses of candidate reservoir species in geographical hot spots for viral emergence is a sensible approach to develop tools to predict, prevent, or contain emergence events. Here, we explore the viruses of Eidolon helvum, an Old World fruit bat species widely distributed in Africa that lives in close proximity to humans. We identified a great abundance and diversity of novel herpes and papillomaviruses, described the isolation of a novel adenovirus, and detected, for the first time, sequences of a chiropteran poxvirus closely related with Molluscum contagiosum. In sum, E. helvum display a wide variety of mammalian viruses, some of them genetically similar to known human pathogens, highlighting the possibility of zoonotic transmission.

Multiple redundant stress resistance mechanisms are induced in Salmonella enterica serovar Typhimurium in response to alteration of the intracellular environment via TLR4 signalling

Toll-like receptor 4 (TLR4) senses bacterial LPS and is required for the control of systemic Salmonella enterica serovar Typhimurium infection in mice. The mechanisms of TLR4 activation and its downstream signalling cascades are well described, yet the direct effects on the pathogen of signalling via this receptor remain unknown. To investigate this we used microarray-based transcriptome profiling of intracellular S. Typhimurium during infection of primary bone marrow-derived macrophages from wild-type and TLR4-deficient mice. We identified 17 S. Typhimurium genes that were upregulated in the presence of functional TLR4. Nine of these genes have putative functions in oxidative stress resistance. We therefore examined S. Typhimurium gene expression during infection of NADPH oxidase-deficient macrophages, which lack normal oxidative killing mechanisms. We identified significant overlap between the 'TLR4-responsive' and 'NADPH oxidase-responsive' genes. This is new evidence for a link between TLR4 signalling and NADPH oxidase activity. Interestingly, with the exception of a dps mutant, S. Typhimurium strains lacking individual TLR4- and/or oxidative stress-responsive genes were not attenuated during intravenous murine infections. Our study shows that TLR4 activity, either directly or indirectly, induces the expression of multiple stress resistance genes during the intracellular life of S. Typhimurium.

Developing sustainable models of rural health care: a community development approach

Globally, small rural communities frequently are demographically similar to their neighbours and are consistently found to have a number of problems linked to the international phenomenon of rural decline and urban drift. For example, it is widely noted that rural populations have poor health status and aging populations. In Australia, multiple state and national policies and programs have been instigated to redress this situation. Yet few rural residents would agree that their town is the same as an apparently similar sized one nearby or across the country. This article reports a project that investigated the way government policies, health and community services, population characteristics and local peculiarities combined for residents in two small rural towns in New South Wales. Interviews and focus groups with policy makers, health and community service workers and community members identified the felt, expressed, normative and comparative needs of residents in the case-study towns. Key findings include substantial variation in service provision between towns because of historical funding allocations, workforce composition, natural disasters and distance from the nearest regional centre. Health and community services were more likely to be provided because of available funding, rather than identified community needs. While some services, such as mental illness intervention and GPs, are clearly in demand in rural areas, in these examples, more health services were not needed. Rather, flexibility in the services provided and work practices, role diversity for health and community workers and community profiling would be more effective to target services. The impact of industry, employment and recreation on health status cannot be ignored in local development.

Salmonella transcriptomics: relating regulons, stimulons and regulatory networks to the process of infection

The advent of Salmonella transcriptomics has heralded a new era for gene expression analysis of this formidable intracellular pathogen. Increasing numbers of Salmonella transcriptomic datasets will contribute to the comprehensive definition of regulons, stimulons and regulatory networks. This task has highlighted the need for sophisticated computational techniques to describe regulatory interactions.

Development and validation of a computerized South Asian Names and Group Recognition Algorithm (SANGRA) for use in British health-related studies

BACKGROUND

Studies on ethnic variations in health have played an important role in aetiological and health services research. Most routine datasets, however, do not include information on ethnicity. South Asians, one of the largest minority ethnic groups in Britain, have distinctive names that also allow differentiation of the main sub-groups with their important differences in health-related exposures and disease risks.

METHODS

A computerized name recognition algorithm (SANGRA) was developed incorporating directories of South Asian first names and surnames together with their religious and linguistic origin. SANGRA was validated using health-related data with self-ascribed information on ethnicity.

RESULTS

SANGRA was successful in recognizing South Asian origin in reference datasets, with sensitivity of 89-96 per cent, specificity of 94-98 per cent, positive predictive value (PPV) of 80-89 per cent and negative predictive value (NPV) of 98-99 per cent. Religious origin was correctly assigned in the majority of cases: sensitivity, specificity and PPV were 94 per cent, 91 per cent and 90 per cent for Hindus; 90 per cent, 99 per cent and 98 per cent for Muslims; and 76 per cent, 99 per cent and 94 per cent for Sikhs. SANGRA correctly identified 76 per cent Gujerati and 70 per cent Punjabi names, although only 62 per cent of Gujerati names were sufficiently distinct to be allocated to the Gujerati-only category and only 53 per cent Punjabi names were allocated to the Punjabi-only category. However, specificity and PPV were high for both languages (respectively 97 per cent and 93 per cent for Gujerati, and 99 per cent and 97 per cent for Punjabi).

CONCLUSIONS

SANGRA provides a practical and valid method of ascertaining South Asian origin by name and, to a lesser degree of accuracy, of differentiating between the main religious and linguistic subgroups living in Britain. This algorithm will be useful in health-related studies where information on self-ascribed ethnicity is not available or is of a limited nature.