Common unity: reconnecting people with the environment through indigenous values and participatory design

<p>A significant problem for struggling communities in New Zealand is disconnection from the environment and a loss of cultural values. These issues cause disengagement and division between the people and the environment. Social stability gradually declines, leading to participation within one’s community being discouraged. Investigations into community engagement and the enhancement of the community environment suggest there has been a failure to address the current issues affecting struggling communities. Disconnect and disregard for Indigenous values in communities prove to be a defining factor in the relationship between people and the environment. Indigenous Māori incorporated Mātauranga (knowledge), Tikanga (customs) and Māori values in their way of life which proved instrumental in their development and sense of Kotahitanga (unity) between themselves and with the environment. This allowed Māori to become one with the land and for Whanaungatanga (sense of belonging) and Kaitiakitanga (guardianship of the land) to spread through the people. However, these values have been compromised and subsequently lost due to the European influence on the land and on Māori people. There needs to be a vigorous search for answers on how to reconnect people with these values so as to build strong and united communities. This design research looks at ways of enhancing the struggling community of Takapūwāhia, Porirua, and the local iwi, Ngāti Toa. It seeks to address problems of disconnect, disengagement and loss of values between the environment and the people. This research aims to answer the research question ‘How can we unite a community by implementing Indigenous values when designing for people?’ The first step will be to undertake a literature review and evaluation of various case studies relevant to the research question. Then community engagement will take place so people can come together to evaluate existing problems and to enable the voice and vision of the people to influence the final design outcome. Effective methods of community engagement will be employed through Participatory and Consultative Design which will provide ways of communicating ideas and solutions. Design experiments will be carried out on the identified problem degraded sites within the Takapūwāhia community. These will be presented back to the community with participation with other community members in the design process, contributing to community growth and identity. With the key objective of the research being to unite the Takapūwāhia community, this will be achieved through their voice and their vision being integral to the design outcome, which will portray a story unique to the people of Ngāti Toa and to Takapūwāhia, exploring Māori symbolism essential to Ngāti Toa and integrating Māori values with Landscape Architecture. This will connect people to the design, this particular place and to the environment and help achieve the goal of the project of creating a sense of unity, ownership and belonging, of Kotahitanga, Whanaungatanga and Kaitiakitanga.</p>

Common unity: reconnecting people with the environment through indigenous values and participatory design

<p>A significant problem for struggling communities in New Zealand is disconnection from the environment and a loss of cultural values. These issues cause disengagement and division between the people and the environment. Social stability gradually declines, leading to participation within one’s community being discouraged. Investigations into community engagement and the enhancement of the community environment suggest there has been a failure to address the current issues affecting struggling communities. Disconnect and disregard for Indigenous values in communities prove to be a defining factor in the relationship between people and the environment. Indigenous Māori incorporated Mātauranga (knowledge), Tikanga (customs) and Māori values in their way of life which proved instrumental in their development and sense of Kotahitanga (unity) between themselves and with the environment. This allowed Māori to become one with the land and for Whanaungatanga (sense of belonging) and Kaitiakitanga (guardianship of the land) to spread through the people. However, these values have been compromised and subsequently lost due to the European influence on the land and on Māori people. There needs to be a vigorous search for answers on how to reconnect people with these values so as to build strong and united communities. This design research looks at ways of enhancing the struggling community of Takapūwāhia, Porirua, and the local iwi, Ngāti Toa. It seeks to address problems of disconnect, disengagement and loss of values between the environment and the people. This research aims to answer the research question ‘How can we unite a community by implementing Indigenous values when designing for people?’ The first step will be to undertake a literature review and evaluation of various case studies relevant to the research question. Then community engagement will take place so people can come together to evaluate existing problems and to enable the voice and vision of the people to influence the final design outcome. Effective methods of community engagement will be employed through Participatory and Consultative Design which will provide ways of communicating ideas and solutions. Design experiments will be carried out on the identified problem degraded sites within the Takapūwāhia community. These will be presented back to the community with participation with other community members in the design process, contributing to community growth and identity. With the key objective of the research being to unite the Takapūwāhia community, this will be achieved through their voice and their vision being integral to the design outcome, which will portray a story unique to the people of Ngāti Toa and to Takapūwāhia, exploring Māori symbolism essential to Ngāti Toa and integrating Māori values with Landscape Architecture. This will connect people to the design, this particular place and to the environment and help achieve the goal of the project of creating a sense of unity, ownership and belonging, of Kotahitanga, Whanaungatanga and Kaitiakitanga.</p>

Polymicrobial synergy stimulates Porphyromonas gingivalis survival and gingipain expression in a multi-species subgingival community

Background Dysbiosis in subgingival microbial communities, resulting from increased inflammatory transudate from the gingival tissues, is an important factor in initiation and development of periodontitis. Dysbiotic communities are characterized by increased numbers of bacteria that exploit the serum-like transudate for nutrients, giving rise to a proteolytic community phenotype. Here we investigate the contribution of interactions between members of a sub-gingival community to survival and development of virulence in a serum environment—modelling that in the subgingival pocket. Methods Growth and proteolytic activity of three Porphyromonas gingivalis strains in nutrient broth or a serum environment were assessed using A600 and a fluorescent protease substrate, respectively. Adherence of P. gingivalis strains to serum-coated surfaces was studied with confocal microscopy and 2D-gel electrophoresis of bacterial supernatants used to investigate extracellular proteins. A model multi-species sub-gingival community containing Fusobacterium nucleatum, Streptococcus constellatus, Parvimonas micra with wild type or isogenic mutants of P. gingivalis was then created and growth and proteolytic activity in serum assessed as above. Community composition over time was monitored using culture techniques and qPCR. Results The P. gingivalis strains showed different growth rates in nutrient broth related to the level of proteolytic activity (largely gingipains) in the cultures. Despite being able to adhere to serum-coated surfaces, none of the strains was able to grow alone in a serum environment. Together in the subgingival consortium however, all the included species were able to grow in the serum environment and the community adopted a proteolytic phenotype. Inclusion of P. gingivalis strains lacking gingipains in the consortium revealed that community growth was facilitated by Rgp gingipain from P. gingivalis. Conclusions In the multi-species consortium, growth was facilitated by the wild-type and Rgp-expressing strains of P. gingivalis, suggesting that Rgp is involved in delivery of nutrients to the whole community through degradation of complex protein substrates in serum. Whereas they are constitutively expressed by P. gingivalis in nutrient broth, gingipain expression in the model periodontal pocket environment (serum) appeared to be orchestrated through signaling to P. gingivalis from other members of the community, a phenomenon which then promoted growth of the whole community.

Grazing Induced Shifts in Phytoplankton Cell Size Explain the Community Response to Nutrient Supply

Phytoplankton cell size is important for a multitude of functional traits such as growth rates, storage capabilities, and resistance to grazing. Because these response traits are correlated, selective effects on mean community cell size of one environmental factor should impact the ability of phytoplankton to cope with other factors. Here, we experimentally apply expectations on the functional importance of phytoplankton cell size to the community level. We used a natural marine plankton community, and first altered the community’s cell size structure by exposing it to six different grazer densities. The size-shifted communities were then treated with a saturated nutrient pulse to test how the changes in community size structure influenced the mean community growth rate in the short-term (day 1–3) and nutrient storage capacity in the postbloom phase. Copepod grazing reduced the medium-sized phytoplankton and increased the share of the smallest (<10 µm3) and the largest (>100,000 µm3). Communities composed of on average small cells grew faster in response to the nutrient pulse, and thus confirmed the previously suggested growth advantage of small cells for the community level. In contrast, larger phytoplankton showed better storage capabilities, reflected in a slower post-bloom decline of communities that were on average composed of larger cells. Our findings underline that the easily measurable mean cell size of a taxonomically complex phytoplankton community can be used as an indicator trait to predict phytoplankton responses to sequential environmental changes.

DeepMicrobeFinder Sorts Metagenomes into Prokaryotes, Eukaryotes and Viruses, with Marine Applications

Sequence classification is valuable for reducing the complexity of metagenomes and providing a fundamental understanding of the composition of metagenomic samples. Binary metagenomic classifiers offer an insufficient solution because metagenomes of most natural environments are typically derived from multiple sequence sources including prokaryotes, eukaryotes and the viruses of both. Here we introduce a deep-learning based (not reference-based) sequence classifier, DeepMicrobeFinder, that classifies metagenomic contigs into five sequence classes, e.g., viruses infecting prokaryotic or eukaryotic hosts, eukaryotic or prokaryotic chromosomes, and prokaryotic plasmids. At different sequence lengths, DeepMicrobeFinder achieved area under the receiver operating characteristic curve (AUC) scores >0.9 for most sequence classes, the exception being distinguishing prokaryotic chromosomes from plasmids. By benchmarking on 20 test datasets with variable sequence class composition, we showed that DeepMicrobeFinder obtained average accuracy scores of ~0.94, ~0.87, and ~0.92 for eukaryotic, plasmid and viral contig classification respectively, which were significantly higher than the other state-of-the-art individual predictors. Using a 1-300 µm daily time-series metagenomic dataset sampled from coastal Southern California as a case study, we showed that metagenomic read proportions recruited by eukaryotic contigs could be doubled with DeepMicrobeFinder’s classification compared to the counterparts of other reference-based classifiers. In addition, a positive correlation could be observed between eukaryotic read proportions and potential prokaryotic community growth rates, suggesting an enrichment of fast-growing copiotrophs with increased eukaryotic particles. With its inclusive modeling and unprecedented performance, we expect DeepMicrobeFinder will promote metagenomic studies of under-appreciated sequence types.

DeepMicrobeFinder sorts metagenomes into prokaryotes, eukaryotes and viruses, with marine applications

Sequence classification is valuable for reducing the complexity of metagenomes and providing a fundamental understanding of the composition of metagenomic samples. Binary metagenomic classifiers offer an insufficient solution because metagenomes of most natural environments are typically derived from multiple sequence sources including prokaryotes, eukaryotes and the viruses of both. Here we introduce a deep-learning based (not reference-based) sequence classifier, DeepMicrobeFinder, that classifies metagenomic contigs into five sequence classes, e.g., viruses infecting prokaryotic or eukaryotic hosts, eukaryotic or prokaryotic chromosomes, and prokaryotic plasmids. At different sequence lengths, DeepMicrobeFinder achieved area under the receiver operating characteristic curve (AUC) scores >0.9 for most sequence classes, the exception being distinguishing prokaryotic chromosomes from plasmids. By benchmarking on 20 test datasets with variable sequence class composition, we showed that DeepMicrobeFinder obtained average accuracy scores of ~0.94, ~0.87, and ~0.92 for eukaryotic, plasmid and viral contig classification respectively, which were significantly higher than the other state-of-the-art individual predictors. Using a 1-300 μm daily time-series metagenomic dataset sampled from coastal Southern California as a case study, we showed that metagenomic read proportions recruited by eukaryotic contigs could be doubled with DeepMicrobeFinder's classification compared to the counterparts of other reference-based classifiers. In addition, a positive correlation could be observed between eukaryotic read proportions and potential prokaryotic community growth rates, suggesting an enrichment of fast-growing copiotrophs with increased eukaryotic particles. With its inclusive modeling and unprecedented performance, we expect DeepMicrobeFinder will be a useful addition to the toolbox of microbial ecologists, and will promote metagenomic studies of under-appreciated sequence types.

Assessing Antibiotics Biodegradation and Effects at Sub-inhibitory Concentrations by Quantitative Microbial Community Deconvolution

Antibiotics in the environment cause widespread concern as a result of their potent inhibitory action on microbial growth and their role in potentially creating selective conditions for proliferation of antibiotic resistant bacteria. Comprising a carbon skeleton, antibiotics should be amenable to microbial biodegradation, but this is still largely uncharted territory because of their simultaneous strong toxicity. In this study, we estimated potential antibiotics degradation by and effects on mixed microbial communities at concentrations sufficiently high to allow sensitive detection of biomass growth, but simultaneously, low enough to mitigate their toxic action. We used three different mixed inoculum sources freshly derived from freshwater, activated sludge or soil, and tested a series of 15 antibiotics from different classes at 1 mg C-carbon l−1 dosage. Consistent community growth was observed for freshwater and activated sludge with ampicillin, erythromycin and chloramphenicol, and with sulfomethoxazole for activated sludge, which was accompanied by parent compound disappearance. Community growth could be attributed to a few subclasses of recognized cell types by using supervised machine-learning-based classifiers. Most other tested antibiotics resulted in inhibition of community growth on background assimilable organic carbon, concomitant with altered composition of the resulting communities. We conclude that growth-linked biodegradation of antibiotics at low concentrations may be present among typical environmental microbiota, but for a selected subset only, whereas for the majority of antibiotics negative effects prevail without any sign of productive growth.