Integration of time-series meta-omics data reveals how microbial ecosystems respond to disturbance.

The development of reliable, mixed-culture biotechnological processes hinges on understanding how microbial ecosystems respond to disturbances. Here we reveal extensive phenotypic plasticity and niche complementarity in oleaginous microbial populations from a biological wastewater treatment plant. We perform meta-omics analyses (metagenomics, metatranscriptomics, metaproteomics and metabolomics) on in situ samples over 14 months at weekly intervals. Based on 1,364 de novo metagenome-assembled genomes, we uncover four distinct fundamental niche types. Throughout the time-series, we observe a major, transient shift in community structure, coinciding with substrate availability changes. Functional omics data reveals extensive variation in gene expression and substrate usage amongst community members. Ex situ bioreactor experiments confirm that responses occur within five hours of a pulse disturbance, demonstrating rapid adaptation by specific populations. Our results show that community resistance and resilience are a function of phenotypic plasticity and niche complementarity, and set the foundation for future ecological engineering efforts.

Hibernoma: A missed diagnosis!!

Hibernoma is a rare, benign soft tissue tumor described in <200 case reports/case series. It is slow-growing, painless, and commonly mistaken for lipoma or liposarcoma. Histopathological diagnosis is must for confirmation. Total excision is the treatment of choice. We present a rare case of hibernoma of thigh, which was initially misdiagnosed as atypical lipomatous tumor/well-differentiated liposarcoma on imaging, which turned out to be a hibernoma on histopathological examination.

The foramen transversarium of typical and atypical cervical vertebrae: morphology and morphometry / El foramen transverso de vértebras cervicales típicas y atípicas: morfología y morfometría

The seven cervical vertebrae found in the human body are classified into typical and atypical vertebrae. Their transverse processes contain foramen transversarium (FT) and traditionally there is one foramen present on each side, of similar size. However, variations of this foramen regarding its shape, size, number, laterality, location and osteometric characteristics have been documented in the literature. This morphological and morphometric study was conducted on 126 cervical vertebrae (82 typical and 44 atypical) obtained from the osteological bank at the University of Kwa-Zulu Natal to produce a database which may serve as a useful guideline to medical personnel. There were variations observed regarding shape, number of FT, laterality and position, which have not previously been reported. The most types of variations were evident in the typical cervical vertebrae, then secondly, the seventh cervical vertebrae. The axis vertebrae did not display any accessory FT or variations.

Las siete vértebras cervicales que se encuentran en el cuerpo humano se clasifican como vértebras típicas y atípicas. Sus procesos transversos presentan un foramen transverso (FT) y normalmente este foramen es de tamaño similar en cada lado. Sin embargo, se han reportado en la literatura variaciones de este foramen, con respecto a su forma, tamaño, número, lateralidad, ubicación y características osteométricas. Este estudio morfológico y morfométrico se realizó en 126 vértebras cervicales (82 típicas y 44 atípicas) obtenidas del banco de Osteología de la Universidad de Kwa-Zulu Natal, para producir una base de datos que pueda servir como una guía útil para el personal médico. Se observaron variaciones con respecto a la forma, el número de FT, la lateralidad y la posición, que no se habían reportado anteriormente. La mayoría de los tipos de variaciones eran evidentes en las vértebras cervicales típicas y en segundo lugar en las séptimas vértebras cervicales. Los axis no mostraron ningún FT accesorio o variaciones.

In situ phenotypic heterogeneity among single cells of the filamentous bacterium Candidatus Microthrix parvicella.

Microorganisms in biological wastewater treatment plants require adaptive strategies to deal with rapidly fluctuating environmental conditions. At the population level, the filamentous bacterium Candidatus Microthrix parvicella (Ca. M. parvicella) has been found to fine-tune its gene expression for optimized substrate assimilation. Here we investigated in situ substrate assimilation by single cells of Ca. M. parvicella using nano-scale secondary-ion mass spectrometry (nanoSIMS). NanoSIMS imaging highlighted phenotypic heterogeneity among Ca. M. parvicella cells of the same filament, whereby (13)C-oleic acid and (13)C-glycerol-3-phosphate assimilation occurred in ≈21-55% of cells, despite non-assimilating cells being intact and alive. In response to alternating aerobic-anoxic regimes, (13)C-oleic acid assimilation occurred among subpopulations of Ca. M. parvicella cells (≈3-28% of cells). Furthermore, Ca. M. parvicella cells exhibited two temperature optima for (13)C-oleic acid assimilation and associated growth rates. These results suggest that phenotypic heterogeneity among Ca. M. parvicella cells allows the population to adapt rapidly to fluctuating environmental conditions facilitating its widespread occurrence in biological wastewater treatment plants.

Integrated omics for the identification of key functionalities in biological wastewater treatment microbial communities.

Biological wastewater treatment plants harbour diverse and complex microbial communities which prominently serve as models for microbial ecology and mixed culture biotechnological processes. Integrated omic analyses (combined metagenomics, metatranscriptomics, metaproteomics and metabolomics) are currently gaining momentum towards providing enhanced understanding of community structure, function and dynamics in situ as well as offering the potential to discover novel biological functionalities within the framework of Eco-Systems Biology. The integration of information from genome to metabolome allows the establishment of associations between genetic potential and final phenotype, a feature not realizable by only considering single 'omes'. Therefore, in our opinion, integrated omics will become the future standard for large-scale characterization of microbial consortia including those underpinning biological wastewater treatment processes. Systematically obtained time and space-resolved omic datasets will allow deconvolution of structure-function relationships by identifying key members and functions. Such knowledge will form the foundation for discovering novel genes on a much larger scale compared with previous efforts. In general, these insights will allow us to optimize microbial biotechnological processes either through better control of mixed culture processes or by use of more efficient enzymes in bioengineering applications.

Lipid-based biofuel production from wastewater.

Increasing world population, urbanization and industrialization are driving global increases in wastewater production. Wastewater comprises significant amounts of chemical energy primarily in the form of organic molecules (in particular lipids), which are currently not being recovered comprehensively. Within biological wastewater treatment (BWWT) systems, specialized microorganisms assimilate and store lipids anaerobically. These intracellular stores represent interesting feedstocks for biofuel synthesis. Here, we review our current understanding of the genetic and functional basis for bacterial lipid accumulation and processing, and relate this to lipid accumulating bacterial populations which occur naturally in BWWT plants. A grand challenge for microbial ecologists and engineers now lies in translating this knowledge into the design of new BWWT processes for the comprehensive recovery of lipids from wastewater streams and their subsequent conversion into biofuel.

A hundred years of activated sludge: time for a rethink.

Biological wastewater treatment plants (BWWTPs) based on the activated sludge (AS) process have dramatically improved worldwide water sanitation despite increased urbanization and industrialization. However, current AS-based operations are considered economically and environmentally unsustainable. In this Perspective, we discuss our current understanding of microbial populations and their metabolic transformations in AS-based BWWTPs in view of developing more sustainable processes in the future. In particular, much has been learned over the course of the past 25 years about specialized microorganisms, which could be more comprehensively leveraged to recover energy and/or nutrients from wastewater streams. To achieve this, we propose a bottom-up design approach, focused around the concept of a "wastewater biorefinery column", which would rely on the engineering of distinct ecological niches into a BWWTP in order to guarantee the targeted enrichment of specific organismal groups which in turn will allow the harvest of high-value resources from wastewater. This concept could be seen as a possible grand challenge to microbial ecologists and engineers alike at the centenary of the discovery of the AS process.

Responses of the coastal bacterial community to viral infection of the algae Phaeocystis globosa.

The release of organic material upon algal cell lyses has a key role in structuring bacterial communities and affects the cycling of biolimiting elements in the marine environment. Here we show that already before cell lysis the leakage or excretion of organic matter by infected yet intact algal cells shaped North Sea bacterial community composition and enhanced bacterial substrate assimilation. Infected algal cultures of Phaeocystis globosa grown in coastal North Sea water contained gamma- and alphaproteobacterial phylotypes that were distinct from those in the non-infected control cultures 5 h after infection. The gammaproteobacterial population at this time mainly consisted of Alteromonas sp. cells that were attached to the infected but still intact host cells. Nano-scale secondary-ion mass spectrometry (nanoSIMS) showed ∼20% transfer of organic matter derived from the infected (13)C- and (15)N-labelled P. globosa cells to Alteromonas sp. cells. Subsequent, viral lysis of P. globosa resulted in the formation of aggregates that were densely colonised by bacteria. Aggregate dissolution was observed after 2 days, which we attribute to bacteriophage-induced lysis of the attached bacteria. Isotope mass spectrometry analysis showed that 40% of the particulate (13)C-organic carbon from the infected P. globosa culture was remineralized to dissolved inorganic carbon after 7 days. These findings reveal a novel role of viruses in the leakage or excretion of algal biomass upon infection, which provides an additional ecological niche for specific bacterial populations and potentially redirects carbon availability.