Whole community shotgun metagenomes of two biological soil crust types from the Mojave Desert

We present six whole community shotgun metagenomic sequencing data sets of two types of biological soil crusts sampled at the ecotone of the Mojave Desert and Colorado Desert in California. These data will help us understand the diversity and function of biocrust microbial communities, which are essential for desert ecosystems.

Metatranscriptomes of two biological soil crust types from the Mojave desert in response to wetting

We present eight metatranscriptomic datasets of light algal and cyanolichen biological soil crusts from the Mojave Desert in response to wetting. These data will help us understand gene expression patterns in desert biocrust microbial communities after they have been reactivated by the addition of water.

Phototrophic Co-cultures From Extreme Environments: Community Structure and Potential Value for Fundamental and Applied Research

Cyanobacteria are found in most illuminated environments and are key players in global carbon and nitrogen cycling. Although significant efforts have been made to advance our understanding of this important phylum, still little is known about how members of the cyanobacteria affect and respond to changes in complex biological systems. This lack of knowledge is in part due to our dependence on pure cultures when determining the metabolism and function of a microorganism. We took advantage of the Culture Collection of Microorganisms from Extreme Environments (CCMEE), a collection of more than 1,000 publicly available photosynthetic co-cultures maintained at the Pacific Northwest National Laboratory, and assessed via 16S rRNA amplicon sequencing if samples readily available from public culture collection could be used in the future to generate new insights into the role of microbial communities in global and local carbon and nitrogen cycling. Results from this work support the existing notion that culture depositories in general hold the potential to advance fundamental and applied research. Although it remains to be seen if co-cultures can be used at large scale to infer roles of individual organisms, samples that are publicly available from existing co-cultures depositories, such as the CCMEE, might be an economical starting point for such studies. Access to archived biological samples, without the need for costly field work, might in some circumstances be one of the few remaining ways to advance the field and to generate new insights into the biology of ecosystems that are not easily accessible. The current COVID-19 pandemic, which makes sampling expeditions almost impossible without putting the health of the participating scientists on the line, is a very timely example.

Metagenomes and metatranscriptomes from boreal potential and actual acid sulfate soil materials

Natural sulfide rich deposits are common in coastal areas worldwide, including along the Baltic Sea coast. When artificial drainage exposes these deposits to atmospheric oxygen, iron sulfide minerals in the soils are rapidly oxidized. This process turns the potential acid sulfate soils into actual acid sulfate soils and mobilizes large quantities of acidity and leachable toxic metals that cause severe environmental problems. It is known that acidophilic microorganisms living in acid sulfate soils catalyze iron sulfide mineral oxidation. However, only a few studies regarding these communities have been published. In this study, we sampled the oxidized actual acid sulfate soil, the transition zone where oxidation is actively taking place, and the deepest un-oxidized potential acid sulfate soil. Nucleic acids were extracted and 16S rRNA gene amplicons, metagenomes, and metatranscriptomes generated to gain a detailed insight into the communities and their activities. The project will be of great use to microbiologists, environmental biologists, geochemists, and geologists as there is hydrological and geochemical monitoring from the site stretching back for many years.

A toolset of constitutive promoters for metabolic engineering of Rhodosporidium toruloides

BACKGROUND

Rhodosporidium toruloides is a promising host for the production of bioproducts from lignocellulosic biomass. A key prerequisite for efficient pathway engineering is the availability of robust genetic tools and resources. However, there is a lack of characterized promoters to drive expression of heterologous genes for strain engineering in R. toruloides.

RESULTS

This data describes a set of native R. toruloides promoters, characterized over time in four different media commonly used for cultivation of this yeast. The promoter sequences were selected using transcriptional analysis and several of them were found to drive expression bidirectionally. Promoter expression strength was determined by measurement of EGFP and mRuby2 reporters by flow cytometry. A total of 20 constitutive promoters (12 monodirectional and 8 bidirectional) were found, and are expected to be of potential value for genetic engineering of R. toruloides.

CONCLUSIONS

A set of robust and constitutive promoters to facilitate genetic engineering of R. toruloides is presented here, ranging from a promoter previously used for this purpose (P7, glyceraldehyde 3-phosphate dehydrogenase, GAPDH) to stronger monodirectional (e.g., P15, mitochondrial adenine nucleotide translocator, ANT) and bidirectional (e.g., P9 and P9R, histones H3 and H4, respectively) promoters. We also identified promoters that may be useful for specific applications such as late-stage expression (e.g., P3, voltage-dependent anion channel protein 2, VDAC2). This set of characterized promoters significantly expands the range of engineering tools available for this yeast and can be applied in future metabolic engineering studies.

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

Standards for sequencing the microbial 'uncultivated majority', namely bacterial and archaeal single-cell genome sequences, and genome sequences from metagenomic datasets, are proposed.

We present two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences. Both are extensions of the Minimum Information about Any (x) Sequence (MIxS). The standards are the Minimum Information about a Single Amplified Genome (MISAG) and the Minimum Information about a Metagenome-Assembled Genome (MIMAG), including, but not limited to, assembly quality, and estimates of genome completeness and contamination. These standards can be used in combination with other GSC checklists, including the Minimum Information about a Genome Sequence (MIGS), Minimum Information about a Metagenomic Sequence (MIMS), and Minimum Information about a Marker Gene Sequence (MIMARKS). Community-wide adoption of MISAG and MIMAG will facilitate more robust comparative genomic analyses of bacterial and archaeal diversity.

Complete genome sequence of Sebaldella termitidis type strain (NCTC 11300)

Sebaldella termitidis (Sebald 1962) Collins and Shah 1986, is the only species in the genus Sebaldella within the fusobacterial family ‘Leptotrichiaceae’. The sole and type strain of the species was first isolated about 50 years ago from intestinal content of Mediterranean termites. The species is of interest for its very isolated phylogenetic position within the phylum Fusobacteria in the tree of life, with no other species sharing more than 90% 16S rRNA sequence similarity. The 4,486,650 bp long genome with its 4,210 protein-coding and 54 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

Association between absence of epidermal growth factor receptor immunoreactivity and poor prognosis in patients with atypical meningioma

OBJECT

The clinical behavior of meningiomas is variable. Because multiple growth factor receptors have been identified in these tumors, the authors sought to assess the capacity of the expression patterns of a subset of these receptors to stratify meningioma cases.

METHODS

Eighty-four meningiomas were analyzed, including 36 benign, 29 atypical, and 19 malignant lesions. Immunohistochemical staining was performed for epidermal growth factor receptor (EGFR), platelet-derived growth factor receptor (PDGFR)-beta, basic fibroblast growth factor receptor (BFGFR), and MIB-1. Survival analyses were performed using follow-up data obtained in patients with newly diagnosed tumors. Immunoreactivity for EGFR was observed in 47% of benign, 48% of atypical, and 42% of malignant tumors. Staining for BFGFR was identified in 89% of benign, 97% of atypical, and 95% of malignant lesions. Immunostaining for PDGFR-beta was evident in all the lesions assessed. Mean MIB-I indices for benign, atypical, and malignant cases were 3.6 (range 0.5-15.3), 8.2 (range 1.5-23.1) and 18.3 (range 1.0-55.8), respectively. Overall mean follow-up duration was 9.0 years (range 5.1-18.8 years). Lack of EGFR immunoreactivity was identified as a strong predictor of shorter overall survival in patients with atypical meningioma (p = 0.003, log-rank test). This association was not evident in cases of benign or malignant meningiomas.

CONCLUSIONS

There is a significant association between EGFR immunoreactivity and prolonged survival in patients with atypical meningioma. Given the variable behavior of atypical meningiomas, EGFR assessment could improve existing strategies for patient stratification and treatment.

Sex steroid and growth factor profile of a meningioma associated with pregnancy

BACKGROUND

Increased growth of meningiomas during pregnancy as well as postpartum clinical regression of symptoms have been reported but remain poorly understood. A better understanding of the factors that contribute to these observations, including potential factors associated with pregnancy, could enable design of more effective adjuvant therapies.

METHODS

We describe the presentation of a meningioma during the immediate postpartum period. Serial imaging demonstrated subsequent rapid decrease in size of the tumour prior to any intervention. The lesion was resected, and the tissue was subjected to immunostaining for gene products associated with pregnancy, including estrogen receptor (ER), progesterone receptor (PR), platelet-derived growth factor receptor B (PDGFRB), fibroblastic growth factor receptor 2 (FGFR-2), epidermal growth factor receptor (EGFR) and human placental lactogen (hPL).

RESULTS

The lesion proved to be an atypical fibroblastic meningioma grade II (WHO). Immunostaining demonstrated significant staining for PR, PDGFRB, and FGFR-2. No specific staining for ER, EGFR, or hPL was identified.

CONCLUSION

Although clinical regression of meningioma following pregnancy is well-recognized, imaging data are much less abundant. This report provides clear clinical and imaging documentation of a meningioma associated with pregnancy. In addition, the growth factor profile of this tumour suggests the importance of PR, PDGFRB, and FGFR-2 as potential therapeutic targets.