A Need for Improved Cellulase Identification from Metagenomic Sequence Data

ABSTRACT Improved sequencing technologies and the maturation of metagenomic approaches allow the identification of gene variants with potential industrial applications, including cellulases. Cellulase identification from metagenomic environmental surveys is complicated by inconsistent nomenclature and multiple categorization systems. Here, we summarize the current classification and nomenclature systems, with recommendations for improvements to these systems. Addressing the issues described will strengthen the annotation of cellulose-active enzymes from environmental sequence data sets—a rapidly growing resource in environmental and applied microbiology.

Advantages and limits of metagenomic assembly and binning of a giant virus

Giant viruses have large genomes, often within the size range of cellular organisms. This distinguishes them from most other viruses and demands additional effort for the successful recovery of their genomes from environmental sequence data. Here we tested the performance of genome-resolved metagenomics on a recently isolated giant virus, Fadolivirus, by spiking it into an environmental sample from which two other giant viruses were isolated. At high spike-in levels, metagenome assembly and binning led to the successful genomic recovery of Fadolivirus from the sample. A complementary survey of viral hallmark genes indicated the presence of other giant viruses in the sample matrix, but did not detect the two isolated from this sample. Our results indicate that genome-resolved metagenomics is a valid approach for the recovery of near-complete giant virus genomes given that sufficient clonal particles are present. Our data also underline that a vast majority of giant viruses remain currently undetected, even in an era of terabase-scale metagenomics.

Complete Genome Sequence of the Environmental Burkholderia pseudomallei Sequence Type 131 Isolate MSHR1435, Associated with a Chronic Melioidosis Infection

ABSTRACT The Burkholderia pseudomallei isolate MSHR1435 is a fully virulent environmental sequence type 131 (ST131) isolate that is epidemiologically associated with a 17.5-year chronic melioidosis infection. The completed genome will serve as a reference for studies of environmental ecology, virulence, and chronic B. pseudomallei infections.

Towards a Better Understanding of Sub-Saharan Settlement Mounds before AD 1400: The Tells of Sadia on the Seno Plain (Dogon Country, Mali)

In the Niger Bend, many studies have shown the existence of settlement mounds which mainly developed between the 1st millennium BC and the 15th century AD. While knowledge about tell-type sites in sub-Saharan Africa has advanced in recent years, many aspects of this topic remain poorly understood. Considering the vast geographic area and time span, there is very little accurate chronostratigraphic information available. This relative lack of long sequences strongly limits the diachronic integration of cultural, economic and environmental data, necessary to unravel the socio-economic mechanisms underlying the emergence and development of this type of site. In this paper, we present the results of the excavations we recently conducted on a group of settlement mounds at Sadia, on the Seno Plain (Dogon Country, Mali), which allow a precise chronological, cultural and environmental sequence to be defined. By combining this work and the results from an extensive approach applied throughout the Dogon Country for more than fifteen years, we provide a scenario for the Seno tells and an insight into the development of Sahelian rural societies, including considerations on their interactions with the early State polities of the Niger Bend, prior to AD 1400.

‘WHERE WATER WELLS UP FROM THE EARTH’: EXCAVATIONS AT THE FINDSPOT OF THE LATE BRONZE AGE HOARD FROM BROADWARD, SHROPSHIRE

The paper begins by considering the importance of springs as a focus for votive deposits in Bronze Age Britain. This is not a new idea, but nowhere has this association been examined through the excavation of one of these features. The point is illustrated by excavation at the findspot of a famous group of Late Bronze Age weapons, the Broadward hoard, discovered in 1867. Little was known about the site, where it was found or the character of the original deposit, but a study of contemporary accounts of the hoard, combined with geophysical and topographical surveys, led to small-scale excavation in 2010, which showed that the deposit had most probably been buried in a pit on the edge of a spring. Other finds associated with the spring included an Early Bronze Age macehead, a Roman pot and various Saxon and medieval animal bones. The latest deposit, with a post-medieval carbon date, included a wooden knife or dagger. An adjacent palaeochannel provided an important environmental sequence for this part of the English–Welsh borderland and suggests that the Late Bronze Age hoard had been deposited not far from a settlement. A nearby earthwork enclosure was associated with a clay weight, which may be of similar date. Despite the limited scale of the fieldwork, it illustrates the potential for treating springs associated with artefact finds on the same terms as other archaeological deposits.