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Общая Биология 79 Общая Биология Удк 579.841:577.21

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Общая Биология 79 Общая Биология Удк 579.841:577.21 Общая биология ОБЩАЯ БИОЛОГИЯ УДК 579.841:577.21 БИОГЕОГРАФИЯ И МОЛЕКУЛЯРНО-ГЕНЕТИЧЕСКИЙ ПОЛИМОРФИЗМ БАКТЕРИЙ РОДА METHYLOPILA, ВЫДЕЛЕННЫХ ИЗ РАЗЛИЧНЫХ КЛИМАТИЧЕСКИХ ЗОН Н.В. Агафонова, Е.Н. Капаруллина, Н.В. Доронина Впервые обнаружены особенности биогеографического распространения ме- тилотрофных бактерий рода Methylopila. Региональная дифференциация выявлена у типовых представителей рода Methylopila: штаммы, выделенные из регионов со сход- ными климатическими условиями, объединены в отдельные филогруппы на основании сравнения нуклеотидных последовательностей гена 16S рРНК. Кроме того, образова- ние аналогичных кластеров в результате филогенетического и фингерпринт (RAPD- PCR) анализов свидетельствует о внутривидовом молекулярно-генетическом поли- морфизме штаммов, принадлежащих к виду M. oligotropha, выделенных из различных природно-климатических регионов. Ключевые слова: метилотрофные бактерии, Methylopila, Methylopila oli- gotropha, молекулярно-генетический полиморфизм, биогеография Род Methylopila, впервые описанный Дорониной с соавторами [1], принадлежит семейству Methylocystaceae [2] порядка Rhizobiales [3]. Представители этого рода являются строго аэробными, грамотрицательными, факультативными метилотрофными бактериями, способными использовать метанол и метиламин в качестве источников углерода и энергии, реализуют сериновый путь С1-метаболизма [1, 4, 5]. В настоящее время валидно описаны следующие виды рода Methylopila (http://www.bacterio.net/methylopila.html): M. capsulata IM1T [1], M. jiangsuensis JZL-4T [5], M. musalis MUSAT [4], M. oligotropha 2395AT [6], M. henanensis LYBFD3-16A2T [7] и M. turkensis Side1T [8, 9], выделенные из природных источников (почвы, растений, подземных вод, активных илов и засоленных биотопов) в различных климатических зонах. Долгое время считалось, что в континентальных масштабах микробные виды не имеют градиента широтного разнообразия, подобных тем, которые наблюдаются у макроскопических видов [10]. Однако еще в прошлом столетии изучение особенностей распространения бактерий рода Bacillus в различных типах почв привело к формированию экогеографического направления почвенной микробиологии [11]. В настоящее время дискуссия по поводу того, демонстрируют ли виды микроорганизмов биогеографический паттерн [12], либо имеют космополитное распространение [13], по-прежнему актуальна. Исследовано географическое распространение для цианобактерий, принадлежащих к родам Synechoccocus [14] и Mastigocladus [15], для термофильных архей Sulfolobus [16] и Pyrococcus [17], для термофильных 79 Известия ТулГУ. Естественные науки. 2019. Вып. 3 бактерий, принадлежащих к родам Roseiflexus [18] и Thermus [19]. Очевидно, что разнообразие микроорганизмов, адаптированных к определенным местообитаниям, определяется экологическими факторами: содержанием органического вещества, влажностью, температурой, кислотностью среды, концентрацией элементов питания и солей. Таким образом, биогеография является важной темой исследования микробных экосистем. C момента описания вида M. oligotropha 2395AT, из образцов почвы, листьев и частей растений различных природно-климатических зон (умеренного, субтропического, экваториального климатических поясов) нами выделены и идентифицированы несколько штаммов, которые, согласно филогенетическому анализу нуклеотидных последовательностей гена 16S рРНК, имели высокий уровень сходства с M. oligotropha 2395AT, выделенным из почвы на территории солеразработок г. Соликамска Пермского края [6]. Цель данной работы – изучение особенностей географического распространения метилотрофных бактерий рода Methylopila и молекулярно-генетического полиморфизма штаммов Methylopila oligotropha, выделенных из различных природно-климатических зон. Материалы и методы Выделение чистых культур и условия культивирования. Объектами исследования служили 9 метилотрофных штаммов, выделенных из образцов почвы, листьев и частей растений различных географически удаленных мест обитания (таблица). Накопительные и чистые культуры выделяли на среде «К» (г/л): KH2PO4 – 2,0; (NH4)2SO4 – 2,0; NaCl – 0,5; MgSO4 · 7H2O – 0,1; FeSO4 · 7H2O – 0,002; pH 7,4 и 0,5% (об/об) метанола, как описано ранее [20]. Чистоту культур проверяли световой микроскопией, а также по однородности колоний на агаризованной среде с метанолом и отсутствию роста на среде LB. В качестве референтных штаммов использовали M. oligotropha 2395AT (VKM B-2788T, CCUG 63805T) и M. capsulata IM1T (VKM B-1606T, ATCC 700716T, DSM 6130T). Изучение культуральных и физиолого-биохимических свойств изолятов. Для описания колоний, изучения морфологии и подвижности клеток штаммы выращивали на агаризованной среде «К» (―Difco‖, США, 2%). Рост изолятов при различных значениях солености (0 – 6 % NaCl) и рН (5,0 – 11,0) исследовали на среде «К». Значения рН устанавливали добавлением 1 М NaOH и 5 н HCl. Образование индола из L-триптофана анализировали с реактивом Сальковского [21]. Калибровочную кривую строили со стандартными растворами индолилуксусной кислоты. 80 Общая биология Штаммы, использованные в работе, источники их выделения и диапазоны (оптимумы) роста рН и солености Регион Источник рН % NaCl Штамм (географические выделения штамма (оптимум) (оптимум) координаты) Территория солеразработок г. Почва, 5м от Соликамск, 5,0 – 10,0 0 – 5,0 2395AТ террикона СКРУ № Россия (8,0 – 8,5) (1,0) 2 (53°38' N, 56°46' E) Засолѐнная почва Троицкий район, Челябинская обл., 5,0 – 10,0 0 – 6,0 2a Троицкого Россия (7,0 – 9,5) (1,0) заказника (53°56' N, 61°14' E) Плоды смородины г. Казань, Россия 5,0 – 10,0 0 – 3,0 RibW красной (Ribes (55°84' N, 49°21' (7,0 – 8,5) (1,0) rubrum L.) E) Почки березы г. Пущино, Московская обл., 5,0 – 10,0 0 – 2,5 1g повислой (Betula Россия (7,5 – 8,0) (1,0) pendula L.) (54°49' N, 37°37' E) Листья лавра г. Анапа, Краснодарский 5,0 – 10,0 0 – 5,0 AnapaLavr благородного край, Россия (44°57' (7,0 – 9,5) (1,0) (Laurus nobilis L.) N, 37°17' E) Листья падуба пгт. Никита, 5,0 – 9,0 0 – 3,0 PadubW остролистного (Ilex Республика Крым, Россия (7,0 – 8,0) (1,0) aquifolium L.) (44°30' N, 34°14' E) Листья полыни г. Севастополь, Республика Крым, 5,0 – 10,0 0 – 4,0 Polyn лечебной (Artemisia Россия (7,0 – 9,0) (1,0) abrotanum L.) (44°36' N, 33°29' E) Мальдивская 5,0 – 11,0 0 – 5,0 M52 Мангровые корни республика (0°35' S, 73°04' E) (7,5 – 8,5) (0,5) Ветки рябины г. Пущино, Московская обл., 5,0 – 10,0 0 – 6,0 Sorbus (Sorbus aucuparia Россия (7,0 – 7,5) (1,5) L.) (54°49' N, 37°37' E) Ризосфера осоки г. Минск, Беларусь 5,5 – 9,5 Minsk 0 – 3 (0,5) (Carex sp. L.) (53°54' N, 27°34' E) (7,0 – 8,0) Микроскопия. Изучение морфологии клеток в режиме фазового контраста проводили с помощью оптического микроскопа Nikon Eclipse Ci 81 Известия ТулГУ. Естественные науки. 2019. Вып. 3 (―Nikon‖, Япония), оснащѐнного камерой ProgRes SpeedXT core5 (―Jenoptik‖, Германия). Выделение и анализ ДНК. ДНК выделяли с использованием набора ZR Fungal/Bacterial DNA MiniPrep (―Zymo Research‖, США) в соответствии с рекомендациями фирмы - производителя. Уровень ДНК- ДНК гомологии штаммов PadubW, 2a, M52 c Methylopila oligotropha 2395AT определяли методом ДНК-ДНК реассоциации [22]. Ген 16S рРНК амплифицировали ПЦР, используя универсальные для прокариот праймеры 27f и 1492r [23]. Продукты реакции разделяли методом электрофореза в 1 %-ном агарозном геле. Выделение и очистку фрагментов ДНК из легкоплавкой агарозы проводили на колонках с использованием набора Zymoclean Gel DNA Recovery Kit (―Zymo Research‖, США), согласно инструкции фирмы-производителя. Секвенирование ПЦР-фрагментов проводили с помощью набора реактивов CEQ Dye Terminator Cycle Sequencing kit (―Beckman Coulter‖, США) на анализаторе CEQ2000 XL (―Beckman Coulter‖, США). Филогенетический анализ. Предварительный филогенетический скрининг сходства последовательностей гена 16S рРНК проводили по базе данных GeneBank [NCBI] с помощью пакета программ BLAST (http://ncbi.nlm.nih.gov). Для более точного определения филогенетического положения изолятов нуклеотидные последовательности генов 16S рРНК выравнивали c последовательностями референтных штаммов ближайших прокариот с помощью программы CLUSTAL W [24]. Филогенетический анализ выполнен при помощи программы MEGA 5 [25]. Филогенетические деревья (филограммы) строили методом присоединения соседей (―neighbor-joining‖) [26]. Статистическую достоверность ветвления оценивали с помощью ―bootstrap-анализа‖ 1000 альтернативных филограмм. Геномный фингерпринт (RAPD-PCR-анализ) (метод случайной амплификации полиморфной ДНК) для выявления генотипических различий между исследуемыми штаммами проводили, используя праймеры BOXA1R [27], GTG5 [28] и OPQ1 [29]. Кластерный анализ продуктов амплификации после разделения методом электрофореза в 1 %- ном агарозном геле выполнен с использованием программы PyElph 1.4 и алгоритма «neighbor-joining» [30]. Результаты и обсуждение Используя метод накопительных культур из проб почвы и частей растений, отобранных из различных географически удаленных мест обитания, выделены чистые культуры метилотрофных бактерий (таблица). Все исследуемые изоляты представлены грамотрицательными, короткими палочками, при росте на агаризованной среде ―К‖ с 0,5% метанола при 29°С образовывали точечные или круглые (1 – 2 мм в диаметре) 82 Общая биология однородные бесцветные колонии с ровным краем, гладкой поверхностью, выпуклым профилем. Спор и простек не образовывали, размножались бинарным делением. Все штаммы росли в жидкой среде с метанолом без агрегации клеток, пигмент не образовывали. На среде с нитратом как источником азота, 0,5 % метанола и 1 % триптофана синтезировали производные индола (3,2 – 5,4 мкг/мл
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