Up-dating the Cholodny method using PET films to sample microbial communities in soil

The aim of this work was to investigate the use of PET (polyethylene terephtalate) films as a modern development of Cholodny’s glass slides, to enable microscopy and molecular-based analysis of soil communities where spatial detail at the scale of microbial habitats is essential to understand microbial associations and interactions in this complex environment. Methods. Classical microbiological methods; attachment assay; surface tension measurements; molecular techniques: DNA extraction, PCR; confocal laser scanning microscopy (CLSM); micro- focus X-ray computed tomography (μCT). Results. We first show, using the model soil and rhizosphere bacteria Pseudomonas fluorescens SBW25 and P. putida KT2440, that bacteria are able to attach and detach from PET films, and that pre-conditioning with a filtered soil suspension improved the levels of attachment. Bacteria attached to the films were viable and could develop substantial biofilms. PET films buried in soil were rapidly colonised by microorganisms which could be investigated by CLSM and recovered onto agar plates. Secondly, we demonstrate that μCT can be used to non-destructively visualise soil aggregate contact points and pore spaces across the surface of PET films buried in soil. Conclusions. PET films are a successful development of Cholodny’s glass slides and can be used to sample soil communities in which bacterial adherence, growth, biofilm and community development can be investigated. The use of these films with μCT imaging in soil will enable a better understanding of soil micro-habitats and the spatially-explicit nature of microbial interactions in this complex environment

Up-dating the Cholodny method using PET films to sample microbial communities in soil

The aim of this work was to investigate the use of PET (polyethylene terephtalate) films as a modern development of Cholodny’s glass slides, to enable microscopy and molecular-based analysis of soil communities where spatial detail at the scale of microbial habitatsis essential to understand microbial associations and interactions in this complex environment. Methods. Classical microbiological methods; attachment assay; surface tension measurements; moleculartechniques: DNA extraction, PCR; confocal laserscanning microscopy (CLSM); micro-focus X-ray computed tomography (µCT). Results. We first show, using the model soil and rhizosphere bacteria Pseudomonas fluorescens SBW25 and P. putida KT2440, that bacteria are able to attach and detach from PET films, and that pre-conditioning with a filtered soil suspension improved the levels of attachment. Bacteria attached to the films were viable and could develop substantial biofilms. PET films buried in soil were rapidly colonised by microorganisms which could be investigated by CLSM and recovered onto agar plates. Secondly, we demonstrate that µCT can be used to non-destructively visualise soil aggregate contact points and pore spaces across the surface of PET films buried in soil. Conclusions. PET films are a successful development of Cholodny’s glass slides and can be used to sample soil communities in which bacterial adherence, growth, biofilm and community development can be investigated. The use of these films with µCT imaging in soil will enable a better understanding of soil micro-habitats and the spatially-explicit nature of microbial interactions in this complex environment. Keywords: Pseudomonas, soil, buried slide, PET film.Мета цієї роботи полягала у дослідженні можливості використання плівок, виготовлених із ПЕТ (поліетилентетрафталат), як модифікації методу скелець обростання Холодного для мікроскопічного і молекулярно-генетичного аналізу ґрунтових спільнот із збереженням їхньої просторової архітектури на мікрорівні. Таке збереження деталей просторового розташування об’єктів дозволило б глибше вивчити їх у подібних складних середовищах проживання. Методи. Класичні мікробіологічні методи; аналіз прикріплення; вимірювання поверхневого натягнення; молекулярно-генетичні методи: екстракція ДНК, ПЛР; конфокальна лазерна скануюча мікроскопія (КЛСМ); мікрофокусна рентгенівська комп’ютерна томографія (мікроКТ). Результати. По-перше, використовуючи модельні ґрунтові і ризосферні бактерії Pseudomonas fluorescens SBW25 і P. putida KT2440, ми показали, що бактерії здатні до прикріплення і відкріплення від ПЕТ плівок, а прекультивація за умов відфільтрованої ґрунтової суспензії покращує рівень прикріплення. Бактерії, які прикріпилися до плівок, зберігають свою життєздатність і спроможні до формування повноцінної біоплівки. ПЕТ плівки, занурені в ґрунт, колонізуються мікроорганізмами, що спостерігали як за допомогою КЛСМ, так і методом культивування ПЕТ плівок, видалених з ґрунту, на агаризованому поживному середовищі. По-друге, ми продемонстрували, що мікроКТ можна використовувати для неруйнівного спостереження сайтів зв’язування ґрунтових агрегатів і ґрунтових пор з поверхнею плівки, що перебуває в ґрунті. Висновки. Застосування ПЕТ плівок виявилося вдалою модифікацією методу скелець обростання Холодного та може бути корисним для відбору ґрунтових мікробних спільнот, дослідження бактерійного прикріплення, росту і розвитку як біоплівок, так і спільноти. Використання цих плівок при аналізі ґрунтів за допомогою мікроКТ дозволить краще визначити ґрунтові мікроеконіші і природу архітектури мікробних взаємодій за таких складних екологічних умов. Ключові слова: Pseudomonas, ґрунт, скельця обростання, ПЕТ плівки.Цель данной работы состояла в исследовании возможности использования плeнок, изготовленных из ПЭТ (полиэтилентерефталат), как современной модификации метода стeкол обрастаний Холодного для микроскопического и молекулярно-генетического анализа почвенных сообществ с сохранением их пространственной архитектуры на микроуровне. Такая сохранность деталей пространственного расположения объектов позволила бы глубже изучить их в подобных сложных условиях обитания. Методы. Классические микробиологические методы; анализ прикрепления; измерение поверхностного натяжения; молекулярногенетические методы: экстракция ДНК, ПЦР; конфокальная лазерная сканирующая микроскопия (КЛСМ); микрофокусная рентгеновская компьютерная томография (микроКТ). Результаты. Во-первых, используя модельные почвенные и ризосферные бактерии Pseudomonas fluorescens SBW25 и P. putida KT2440, мы показали, что бактерии способны к прикреплению и откреплению от ПЭТ плeнок, а прекультивирование в условиях отфильтрованной почвенной суспензии улучшает уровень прикрепления. Бактерии, прикреплeнные к плeнкам, сохраняют жизнеспособность и могут формировать полноценную биоплeнку. ПЕТ плeнки, погружeнные в почву, колонизируются микроорганизмами, что наблюдали как с применением КЛСМ, так и методом культивирования извлечe нных из почвы плeнок на агаризованной питательной среде. Во-вторых, мы продемонстрировали, что микроКТ можно использоватьа для недеструктивного наблюдения за сайтами связывания почвенных агрегатов и почвенных пор с поверхностью ПЕТ плeнки, находящейся в почве. Выводы. Применение ПЕТ плeнок оказалось удачной модификацией метода стeкол обрастаний Холодного и может стать полезным для отбора почвенных микробных сообществ, изучения бактериального прикрепления, роста, развития как биоплeнок, так и сообщества. Использование этих плeнок при анализе почвы с помощью микроКТ позволит лучше определять почвенные микроэкониши и природу архитектуры микробных взаимодействий в таких сложных экологических условиях. Ключевые слова: Pseudomonas, почва, стeкла обрастания, ПЭТ плeнки

A PXI based implementation of a TLK2711 equivalent interface

In the last few years, satellite on board data handling data rate requirements increased dramatically, from hundreds of megabits per second to several gigabits per second. SpaceWire, the current generation European standard communication protocol, is no more able to satisfy the demanding requirements, while the upcoming protocol, SpaceFibre, has not been adopted yet in any current space missions. This resulted in the adoption by the industry and by space agencies of a non-standardized solution, the TLK2711 ASIC chip, which implements lower communication protocol levels of the Open System Interconnection stack (Wizard Link), leaving to the user the implementation of higher-level stack layers. Consequently in the space community the need for hardware to test these systems grown. In this paper, an implementation of a Wizard Link TLK2711 equivalent circuit on a National Instruments PXI platform is presented, in order to boost the development of TLK2711 compatible ground test equipment

Design of a spacewire/spacefibre EGSE system based on PXI industry standard

This paper introduces a comprehensive test equipment for early adopters of the new ECSS satellite on-board serial high-speed communication protocol, SpaceFibre, maintaining also retro-compatibility with its precursor, SpaceWire. The presented system is based on the PCI eXtension for Instrumentation (PXI) industry standard and designed with cutting edge high level synthesis techniques. It offers support in development of both SpaceWire and SpaceFibre devices, even in cross standard communication, for current and future generation spacecraft missions. Thanks to its native integration in the PXI platform, the proposed Electrical Ground Segment Equipment (EGSE) system is ready to be integrated out of the box in larger prior existing testing and simulation environment

Exploiting LabVIEW FPGA Socketed CLIP to Design and Implement Soft-Core Based Complex Digital Architectures on PXI FPGA Target Boards

PXI FPGA Peripheral Modules by National Instruments are meant to be used in LabView even without any previous knowledge of Hardware Description Languages (HDL) and let users to hardware-accelerate their own test and measurement setups. However, designers fluent in HDL languages avoid such closed technology targets due to impossibility to include third-party designs or the needed over-effort to implement large and complex architectures into it, such as soft-core based systems. In this paper a partially automated workflow to benefit of the PXI environment allowing advanced HDL engineers to implement complex architectures is presented with reference to two successful use-case examples

Design of a SpaceFibre High-Speed Satellite Interface ASIC

In the last few years, data rate requirement in on-board data handling for space missions has continuously grown, due to the presence of high resolution instruments. This lead the European Space Agency to start working on a new communication standard named SpaceFibre. It is able to fulfil a data rate of 6.25 Gbit/s per communication lane (up to 16 communication lanes). This work proposes the design of a SpaceFibre interface Application Specific Integrated Circuit. The block diagram of the system is presented, together with results in terms of area occupation and power consumption (excluding serialiser-deserialiser circuitry) after the synthesis on a 65 nm CMOS technology

AXI4LV: Design and Implementation of a Full-Speed AMBA AXI4-Burst DMA Interface for LabVIEW FPGA

The Advanced Microcontroller Bus Architecture Advanced eXtensible Interface is a memory mapped protocol intended for internal System on Chip communications. However, there is no mean to directly exchange data between AXI devices and LabVIEW applications. This work proposes a novel and streamlined bridge solution to transfer data directly and effectively from/to an AXI target memory and any LabVIEW FPGA application, essential to integrate AXI-based architectures into PXI FPGA peripheral modules. The block diagram of the proposed IP solution and synthesis results are presented for target programmable devices of interest

The very high-speed SpaceFibre multi-lane CoDec: Implementation and experimental performance evaluation

On-board data handling sub-systems shall provide robust communication on-board spacecraft and have strict requirements in terms of reliability, fault-tolerance and redundancy. In the next years, on-board data handling sub-systems will be required to sustain high-speed payloads since satellites will host new high-resolution instruments, requiring a multi-gigabit data rate. The European Space Agency promotes the usage of a standard for the implementation of a very high-speed link for satellite on-board data-handling, SpaceFibre, that supports multi-lane communication links. Indeed, due to the stringent requirements of future on-board data handling subsystems, it will be necessary to have links that include more lanes to enhance system reliability and bandwidth. SpaceFibre aims at becoming the state-of-the-art for future on-board data handling subsystem, combining high-speed with high reliability and fault tolerance capability. In this paper, we introduce and report the development of an innovative multi-lane SpaceFibre core, and compares it with other promising space-oriented standards regarding multi-lane features. We present the results of a test campaign that aims at measuring SpaceFibre multi-lane performances in terms of recovery time after a lane failure, observing that the communication process can be completely restored between 4.42 μs and 6.30 μs. Implementation results on state-of-the-art space-oriented FPGAs, such as the Microsemi RTG4 and the Xilinx UltraScale Virtex KU060 are also included. Finally, we carry out a detailed power consumption analysis, including results for different core configurations, measuring the SpFi dynamic power consumption contribution to be between 576.7 mW and 148.4 mW for target configurations on a Microsemi RTG4

Integration of a SpaceFibre IP Core with the LEON3 Microprocessor Through an AMBA AHB Bus

Nowadays, requirements for satellite electronics are becoming more stringent due to the increasing complexity of space missions. In particular, data rate requirement is growing up due to the adoption of high-speed payloads such as Synthetic Aperture Radars and hyper-spectral imagers that overcome the capability of state-of-the-art on-board data handling system. The European Space Agency answered to this request introducing a new high-speed communication protocol, SpaceFibre. At the same time, data collected by high-speed interfaces may be processed on-board with specific hardware or general-purpose microprocessor such as the LEON3. The aim of this paper is to describe the integration of a SpaceFibre IP core in the Cohbam Gaisler GRLIB library, to integrate the functionalities offered by the SpaceFibre CODEC with the potential of the LEON3 microprocessor. Implementation results on a Xilinx Virtex-6 and an analysis of the performance of the SpaceFibre interface on an AMBA 2.0 AHB bus are presented

A complete egse solution for the spacewire and spacefibre protocol based on the pxi industry standard

This article presents a complete test equipment for the promising on-board serial high-speed SpaceFibre protocol, published by the European Committee for Space Standardization. SpaceFibre and SpaceWire are standard communication protocols for the latest technology sensor devices intended for on-board satellites and spacecrafts in general, especially for sensors based on image acquisition, such as scanning radiometers or star-tracking devices. The new design aims to provide the enabling tools to the scientific community and the space industry in order to promote the adoption of open standards in space on-board communications for current-and future-generation spacecraft missions. It is the first instrument expressly designed for LabVIEW users, and it offers tools and advanced features for the test and development of new SpaceFibre devices. In addition, it supports the previous SpaceWire standard and cross-communications. Thanks to novel cutting-edge design methods, the system complex architecture can be implemented on natively supported LabVIEW programmable devices. The presented system is highly customizable in terms of interface support and is provided with a companion LabVIEW application and LabVIEW Application Programming Interface (API) for user custom automated test-chains. It offers real-time capabilities and supports data rates up to 6.25 Gbps.The proposed solutions is then fairly compared with other currently available SpaceFibre test equipment. Its comprehensiveness and modularity make it suitable for either on-board device developments or spacecraft system integrations